PyMOL Wiki - User contributions [en]

Main Page

2009-09-13T19:32:08Z

Warren:

__NOTOC__
{| align="center" width="90%"
|+ style="font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
| ''The community-run support site for the [http://pymol.org PyMOL] molecular viewer.''
|-
|}
{| align="center" style="width:90%; margin-bottom: 20px"
|
{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
|-
| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to [[Special:Userlogin|join]]. Feel free to add any appropriate content; make an account and [[PyMolWiki:Community_Portal|get started]]!
|-
|}
{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
|-
| [[TOPTOC|'''Table of Contents''']]
|| [[Special:Allpages|Index of all pages]]
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
|-
| [[:Category:Tutorials|Tutorials]] !
|| [[:Category:Commands|Commands]]
|| '''Settings''': [[Settings|All]] | [[:Category:Settings|Documented]]
|-
| [[:Category:Script_Library|'''Script Library''']] !
|| [[:Category:Plugins|'''Plugins''']]
|| [[:Special:Categories| See All Categories]]
|-
| [[:Category:FAQ|Frequently Asked Questions]]
|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
|| [[About| '''About PyMOL''']]
|-
| ''Track:'' [http://sourceforge.net/tracker/?atid=104546&group_id=4546&func=browse Bugs] [http://sourceforge.net/tracker/?group_id=4546&atid=354546 Feature Req] [http://sourceforge.net/tracker/?group_id=4546&atid=204546 Support Req]
|-
|}
|- style="color: #333; font-weight:bold; font-size: 20px; text-align:center; padding: 10em;"
|

|
|}
{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
|+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]])
|
{|style="background-color: transparent;" width="100%"
|-
|valign="top"|
{|style="background-color: transparent;" width="100%"
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
|-
| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL is known to work under Mac OS X 10.6 (Snow Leopard) using the new Fink. See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
|-
| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Space]]— new command to control PyMOL's usage of color spaces.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CGOCylinder]]— information on CGO cylinders and circles in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''[http://www.pymol.org/ PyMOL] 1.2 is out!
|-
| style="padding: 2px 5px 0px 15px;"| &diams; Check out the artist who integrates PyMOL into [http://winkleman.com/artist/seriesview/1406/376 his work].
|-
| style="padding: 2px 5px 0px 15px;"| &diams; If you use the sequence viewer alot, or have lots of openGL text on the screen, try boosting your performance with [[Texture_fonts]].
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''PyMOL now integrates seamlessly with MS Powerpoint. See [[Axpymol]].'''
|}
|valign="middle" width="150px" style="padding: 0 20px 20px 0" |[[Image:080602cnen.pdf.jpg|125px]] Another cover made with PyMOL. See [[Covers]].
|}
|-
|
{|style="background-color: transparent;" width="100%"
|-
|valign="top"|
{|style="background-color: transparent;" width="100%"
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts, Plugins & Tutorials
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Spectrumbar]]— powerful new script for making custom spectrum bars in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CollapseSel]]— simple script to compress selection lists: eg. instead of i. 1+2+3+4+5 you get 1-5.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[SuperSym]]— incredible script for handling crystallographic symmetry operations.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CgoCircle]]— draw CGO circles in PyMOL; surround objects or selections with circles.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[MovieSchool]] — PyMOL Wiki's Movie School. Learn how to make movies in PyMOL!
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[alphaToAll]] — Expands your desired alpha-carbon property down to all atoms in the residue.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[interfaceResidues]] — Finds interface residues in a complex.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSurfaceResidues]] — Find and show (if you want) surface exposed resiues in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[ToGroup]] — Converts a multistate object into a group of single state objects.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSeq]] — Find sequence or regular expression of amino acids in a protein.
|-
| style="padding: 2px 5px 10px 15px;"| &diams; [[Modevectors]] — creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
|}
|valign="middle" width="150px" style="padding: 0 20px 20px 0" |[[Image:Sb_default.png|165px]] Example image from the new script, [[Spectrumbar]].
|}
{|style="background-color: transparent;" width="100%"
|-
|valign="top"|
{|style="background-color: transparent;" width="100%"
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Label]]s page was thoroughly refurbished.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance. The downtime was <10 minutes.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''Please note the "Go" and "Search" buttons in the search bar. They're not the same, and entering text and hitting ENTER is the same as using the "Go" button.''' Please try using the "Search" button; we're using a new search engine and it has cool new features.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; Documented a few more settings. Also, check out the cool, [[Huge_surfaces]] page for handling very large objects and representing them as surfaces, in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:Science090410.jpg|125px]] Sample Cover from the [[Covers]] gallery.
|}
|}

Main Page

2009-09-13T19:29:24Z

Warren:

__NOTOC__
{| align="center" width="90%"
|+ style="font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
| ''The community-run support site for the [http://pymol.sf.net PyMOL] molecular viewer.''
|-
|}
{| align="center" style="width:90%; margin-bottom: 20px"
|
{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
|-
| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to [[Special:Userlogin|join]]. Feel free to add any appropriate content; make an account and [[PyMolWiki:Community_Portal|get started]]!
|-
|}
{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
|-
| [[TOPTOC|'''Table of Contents''']]
|| [[Special:Allpages|Index of all pages]]
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
|-
| [[:Category:Tutorials|Tutorials]] !
|| [[:Category:Commands|Commands]]
|| '''Settings''': [[Settings|All]] | [[:Category:Settings|Documented]]
|-
| [[:Category:Script_Library|'''Script Library''']] !
|| [[:Category:Plugins|'''Plugins''']]
|| [[:Special:Categories| See All Categories]]
|-
| [[:Category:FAQ|Frequently Asked Questions]]
|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
|| [[About| '''About PyMOL''']]
|-
| ''Track:'' [http://sourceforge.net/tracker/?atid=104546&group_id=4546&func=browse Bugs] [http://sourceforge.net/tracker/?group_id=4546&atid=354546 Feature Req] [http://sourceforge.net/tracker/?group_id=4546&atid=204546 Support Req]
|-
|}
|- style="color: #333; font-weight:bold; font-size: 20px; text-align:center; padding: 10em;"
|

|
|}
{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
|+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]])
|
{|style="background-color: transparent;" width="100%"
|-
|valign="top"|
{|style="background-color: transparent;" width="100%"
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
|-
| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL is known to work under Mac OS X 10.6 (Snow Leopard) using the new Fink. See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
|-
| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Space]]— new command to control PyMOL's usage of color spaces.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CGOCylinder]]— information on CGO cylinders and circles in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''[http://www.pymol.org/ PyMOL] 1.2 is out!
|-
| style="padding: 2px 5px 0px 15px;"| &diams; Check out the artist who integrates PyMOL into [http://winkleman.com/artist/seriesview/1406/376 his work].
|-
| style="padding: 2px 5px 0px 15px;"| &diams; If you use the sequence viewer alot, or have lots of openGL text on the screen, try boosting your performance with [[Texture_fonts]].
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''PyMOL now integrates seamlessly with MS Powerpoint. See [[Axpymol]].'''
|}
|valign="middle" width="150px" style="padding: 0 20px 20px 0" |[[Image:080602cnen.pdf.jpg|125px]] Another cover made with PyMOL. See [[Covers]].
|}
|-
|
{|style="background-color: transparent;" width="100%"
|-
|valign="top"|
{|style="background-color: transparent;" width="100%"
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts, Plugins & Tutorials
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Spectrumbar]]— powerful new script for making custom spectrum bars in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CollapseSel]]— simple script to compress selection lists: eg. instead of i. 1+2+3+4+5 you get 1-5.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[SuperSym]]— incredible script for handling crystallographic symmetry operations.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CgoCircle]]— draw CGO circles in PyMOL; surround objects or selections with circles.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[MovieSchool]] — PyMOL Wiki's Movie School. Learn how to make movies in PyMOL!
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[alphaToAll]] — Expands your desired alpha-carbon property down to all atoms in the residue.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[interfaceResidues]] — Finds interface residues in a complex.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSurfaceResidues]] — Find and show (if you want) surface exposed resiues in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[ToGroup]] — Converts a multistate object into a group of single state objects.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSeq]] — Find sequence or regular expression of amino acids in a protein.
|-
| style="padding: 2px 5px 10px 15px;"| &diams; [[Modevectors]] — creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
|}
|valign="middle" width="150px" style="padding: 0 20px 20px 0" |[[Image:Sb_default.png|165px]] Example image from the new script, [[Spectrumbar]].
|}
{|style="background-color: transparent;" width="100%"
|-
|valign="top"|
{|style="background-color: transparent;" width="100%"
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Label]]s page was thoroughly refurbished.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance. The downtime was <10 minutes.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''Please note the "Go" and "Search" buttons in the search bar. They're not the same, and entering text and hitting ENTER is the same as using the "Go" button.''' Please try using the "Search" button; we're using a new search engine and it has cool new features.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; Documented a few more settings. Also, check out the cool, [[Huge_surfaces]] page for handling very large objects and representing them as surfaces, in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:Science090410.jpg|125px]] Sample Cover from the [[Covers]] gallery.
|}
|}

User:Inchoate

2009-06-12T22:25:07Z

Warren: /* Terminology */

My name is Jason Vertrees and I'm a postdoc in computational biology. Currently, I study proteins through mathematical models & machine learning. My previous work was in theoretical biophysics.

Also, I am the owner and of the PyMOLWiki website.

If you are interested in Biophysical, Structural or Compuational Biology, check out [http://www.bscb.utmb.edu/ BSCB@UTMB] -- my old school.

'''Jason Vertrees, PhD

''jv(_at-)cs_dot_dartmouth(dot2)edu''

[http://www.cs.dartmouth.edu/~jv/ My Page]

= My ~/.pymolrc =
<source lang="python">
run ~/playground/pymol_scripts/oload.py
run ~/playground/cealign/qkabsch.py
run ~/playground/cealign/cealign.py
run ~/playground/pymol_scripts/find_bind.py
run ~/playground/pymol_scripts/zero.py
run ~/playground/pymol_scripts/removeAlt.py
run ~/playground/pymol_scripts/toGroup.py

one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', \
'GLY':'G', 'PRO':'P', 'CYS':'C'}

set ribbon_width, 8
set antialias,2
set cartoon_fancy_helices,1
set ray_trace_mode,1
set depth_cue,0
set ray_trace_fog,0
set ray_opaque_background,0
set defer_builds_mode, 3
</source>

== To Do ==
* texture_fonts, 1 -- for speed
* pseudo-atoms; you can label them. RightClick->New->PAtom->and then label it; move the atom (and the label goes w/it). You can also move the label by itself
* movie_panel
* mset - clears the movie
* Movie->UpdateMovie
* Scene->Buttons (shows buttons for each scene)
* Scene->Optmize (before saving scenes; use before optimizing)
* Scene->Cache (cache's surface data)
* A good way to make movies seems to be:
** madd
** prepare a scene; turn on scene buttons
** Fn+CTRL+down-arrow # adds the scene;
** madd 1 x90
** mview store, -1
* repeat
* when done do mview reinterpolate
* play the movie
* matrix_mode
* dot_solvent

=== Movie Notes ===
<source lang="python">
#
# Simple movie of independent motions
#

# This create an ala and a tyr. It moves the ala indepdendent
# of the tyr.
#
# Q: Why are the orientations off? What is the equivalent
# command to moving something with mouse_motions?

# reinit
reinitialize

set matrix_mode, 1
# turns on handy scene buttons
set scene_buttons, 1
# turns on the movie panel at the bottom of the sceen
set movie_panel, 1
# turns on a special mouse button panel
config_mouse three_button_motions

# start with an empty movie, scene 1 with 90 frames
mset 1 x90

# create an ala and tyr
frag ala
frag tyr
as spheres

# create our scene
translate [10, 0, 0], object=ala, camera=0
orient

# store the first frame
frame 1
mview store, object=ala

# goto the next frame
frame 45
translate [-20, 0, 0], object=ala, camera=0
orient

# store this frame
mview store, object=ala

#reinterpolate the scene
mview reinterpolate, object=ala
</source>

= Movie Making =
While PyMOL's capability to produce static images is quite powerful, there are some stories that are better told through movies, than static images alone. This little page will provide the necessary ideas, links, code and examples for making movies in PyMOL.

== Your First Movie ==
Movies can be very simple, for example, animating an NMR ensemble:
<source lang="python">
# Your first movie.
fetch 1nmr
mplay

# to stop the movie when you're ready
# type 'mstop'.
</source>

What PyMOL did here was to [[fetch]] the file from the PDB and load it into an object with 20 states. Somewhere between then and issuing [[mplay]] PyMOL created 20 frames for your object and assigned one state to each frame. This created the animated effect as we scroll through the frames.

== Terminology ==
Imagine a complex movie for a moment, a movie that has camera motions, objects moving independently or in concert with other objects, changing colors and representations. To handle camera motions PyMOL must know at all times where the camera is located and what it's pointed toward (as well as clipping planes). For objects to move around or be rotated without regard to the camera (the objects themselves rotate/translate, not just the camera), PyMOL has to store the coordinates and matrices for these objects, too. Changing colors and representations for each object must somehow also be stored. So, as you can see this is a multidimensional problem: at each time point in your movie, PyMOL must remember positions and representations, as well as make it easy for you to transition between them (interpolation).

Despite these complexities, PyMOL tries to enable movie making for even novice users. Let's start by defining a few PyMOL concepts—states, frames and scenes.

=== Basic Movie Terminology ===
'''object'''
::An object is any PyMOL-object loaded into PyMOL, like atoms, molecules, complexes, etc. When you load an PDB from disk/net it is loaded into PyMOL as an object.
:: [[:Category:Objects|All pages regarding objects]]

'''selection'''
:: A selection is a specifically chosen set of atoms, molecules, complexes etc. in PyMOL. A selection is not an object, it's a subset of stuff from a (collection of) object(s). Selections can be named and when named have are distinguished from objects by having parentheses around their names. For example, ''foo'' would be an object and ''(foo)'' would be some selection. When you pick an atom (and get the default '''(sele)''' selection) or issue the ever-popular [[Select]]ion command, you get a selection.
:: [[:Category:Selections|All pages regarding selections]]

'''states'''
:: A state is a particular conformation (set of coordinates) for a given object. For example an NMR ensemble could contain the same molecule, but in 20 different states. PyMOL can make movies from states. States '''do not store representations''' in PyMOL (eg. cartoons vs. sticks).
:: See also [[:Category:States|All pages regarding states]]

'''scenes'''
'''interpolation'''
:: A scene is the staged representations of objects and the orientation of the camera.
:: See also [[:Category:Scenes|All pages regarding scenes]]

'''frames'''
:: A frame can be thought of as a single frame in a movie reel. A frame stores state information and scene information.
:: See also [[:Category:Frames|All pages regarding frames]]

'''Movie Panel'''
:: The movie panel is a frame indicator strip at the bottom of the screen. It shows a little icon for which frame you're currently on, and whether or not the camera has been set for that frame.
:: See [[movie_panel]] for more information.

== What is a Movie? ==
Now the we have the appropriate terminology to talk about movies in PyMOL, we can discuss what a movie really is. A movie in PyMOL is a series of frames stitched together in some way so as to create the desired animation.

== Movie Making Commands ==
This tutorial assumes you have some basic knowledge about how to use PyMOL (eg. mousing, choosing and setting your representations, etc). If you're not yet at this level, please check out [[:Category:Tutorials|the Tutorial Category]] of pages (most notably the beginner tutorials).

I think it's help to think of the movie as a set of frames, like in a movie reel, so let's start there. (Each command below links to the command's PyMOL wiki page, so feel free to click through for more info.)

=== [[frame]]===
This command tells PyMOL to set the current frame to whichever you desire. To use it, just issue the command, <source lang="python">frame X</source> where '''X''' is some integer number indicating the frame you want to go to. If you issue a frame number greater than the number of frames, PyMOL sets the frame to the highest-numbered frame you have (similarly for negative numbers or numbers smaller than the minimum numbered frame).

Let's try a quick example with [[frame]],
<source lang="python">
# create an empty 90 frame movie
mset 1 x90
# turn on the movie panel (bottom of screen)
set movie_panel, on
# goto frame one
frame 1
# try some intermediate frames; notice the blue indicator in the movie panel
frame 10
frame 50
frame 90
# try going beyond the end and see what PyMOL does
frame -1
frame 100
# play through the empty movie
mplay
# stop the movie
mstop
</source>

=== [[States|set state]] ===
Again, states are particular stored conformations of objects. Here we use PyMOL to set and get the states, and see how PyMOL mapped them to our earlier movie example.

This command has a similar idea of [[frame]], but works a little differently. Instead of typing,
<source lang="python">
# invalid command
state 40
</source>
in PyMOL we [[set]] the [[States|state]]:
<source lang="python">
# how to set a state in PyMOL
set state, stateNo, objectName

# for example
# set state to 40
set state, 40

# also, get state
get state
</source>

==== States & Frames (optional reading) ====
As an example, look at the code from the "first movie":
<source lang="python">
fetch 1nmr
mplay
# issue mstop, to stop the movie
</source>

We can do a couple things now, let's try counting the number of states and frames PyMOL now knows about:
<source lang="python">
# how many frames does PyMOL know about?
count_frames

# what about states?
count_states
</source>

and now let's see how PyMOL mapped frames to states. Using the above commands and a little Python, let's see how PyMOL mapped the frames to states:
<source lang="python">
python
for x in range(1,cmd.count_frames()+1):
cmd.frame(x)
print "Frame => %s; and State => %s" % ( str(x), str(cmd.get('state')))
python end
</source>
which should show a 1-1 mapping of states to frames.

=== [[mset]] ===
[[mset]] is a very powerful command. This command tells PyMOL how to assign states to frames. So, now you see why it's necessary to clearly distinguish between and use the two. Let's learn how to use [[mset]].

The syntax for [[mset]] can be a little tricky at first. I would write the syntax as:
<source lang="python">
mset stateSpec frameSpec
</source>
which assigns the states in '''stateSpec''' to the frames in '''frameSpec'''., where '''stateSpec''' is any mset-valid state specification. PyMOl supports to patterns for '''stateSpec'''. You can do simply supply a number eg
<source lang="python">
mset 1
</source>
or you can specify a range of states—like 1 through 55 as
<source lang="python">
# setting states 1 through 55
# caution: notice the space: 1 -55, not 1-55 (this is a PyMOL parser caveat)
mset 1 -55
</source>
Simple enough. Now for '''frameSpec''' you can specify a single frame number like so or you can specify ''how many frames PyMOL should use to map to your specified states'' with the '''xNumber'' command. This will make sense with an example
<source lang="python">
# Recall: mset stateSpec frameSpec
# so we are setting STATE 1 across a span of 90 frames
mset 1 x90

# Recall: mset stateSpec frameSpec
# so we are setting states 1..120 to the next 120 frames
mset 1 -120 x120
</source>

NB: Actually the syntax is a little more complicated than this as PyMOL's mset command has the ability to remember in which frame the prior specification left the movie. So, you can sort of chain the specifications. Type ''help mset'' in PyMOL for more info or see [[mset]].

=== [[mview]] ===
The [[mview]] command can be intimidating, but all we need to know about it at present is that it can store the (1) camera position or (2) a given object position. The idea is to essentially make 'way points' in your movie and have PyMOL interpolate the in-between positions/coordinates, etc. For example, if I wanted to make a 100-frame movie of a zoom into an object, I could store and manually set 100 camera positions, or I could do the starting position and the final position and ask PyMOL to just interpolate that over 100 frames. The latter idea is obviously much simpler. So simple in fact, let's make a super-quick movie that does exactly what I just mentioned—100 frames of a slow zoom into some object. Start with a fresh PyMOL session ([[reinitialize]]) and then copy/paste the following:
<source lang="python" line=1>
# let's initialize the movie to 100 frames, all of state 1
# it's ONLY state 1, because we're only moving the camera around, not
# changing structure coordinates of the leucine:
mset 1 x100

# show a leucine
frag leu

# position the residue
orient

# let's store the current camera position
mview store

# now set our way point to be frame 100
frame 100

# now let's zoom into some atom on the fragment
zoom ID 10

# now save this view at frame 100
mview store

# last thing is to tell PyMOL to interpolate the 100 frame zoom
# so we don't have to do those 100 snapshots:
mview reinterpolate

# voila, you have a movie. To watch it go back to frame 1 and play it
frame 1
mplay

# mstop when you're ready
</source>

'But, hold on!' you might say. Why is it so herky-jerky? We have smooth zooming but then a snap and back to frame one! Well, we never gave PyMOL any number of frames to interpolate the change from frame 100 back to frame 1 (since it wraps). If we wanted an a '''zoom in''' that was equally as fast as the '''zoom out''' we would simply '''replace line #16''' with
<source lang="python">
# now set our way point to be frame 100
frame 100
</source>
but, if we wanted a slow, zoom in and a ''fast'' zoom out we could do
<source lang="python">
# now set our way point to be frame 100
frame 80
</source>
instead which would only give PyMOL 20 frames with which to zoom us out. Try it!

==== Very Basic Mview Syntax ====
''This is a simple overview, see [[mview]] for complete details.''

Using [[mview]] as you can see from above is pretty simple. The very basic syntax is:
<source lang="python">
# store the camera OR some object given by objName (if it's supplied)
mview store[, object=objName]

# reinterpolate (link together the positions) for the saved camera or object
mview reinterpolate[, object=objName]
</source>
If you leave off the '''object=objName''' then you're storing the '''camera information only'''—and so none of your objects will be moving anywhere—just the camera. If you include an object name, then it stores that object's position information in the current frame. The '''mview store''' tells PyMOL to store the camera or objects coordinates, while the '''mview reinterpolate''' command tells PyMOL to link together the saved positions for the camera or the selected object in a smooth, cool way.

== Simple Movie Examples ==
We now the ability to make some pretty simple, but cool movies. So, let's try a few.

=== Multiple Zooming ===
Let's try making a movie where we zoom into each ligand that's not water. In order to make this movie, I had to find a protein with suitable ligands, so you can do the same for your own protein. Just replace the hard-coded residue numbers.

'''Goal:''' Make a movie that zoom into the three ligands, stays on that ligand for 2 seconds, then moves to the next. I also want smooth zoom out at the end. Don't let the length of this movie script throw you off, you've seen all of the movie commands and the initial commands are just loading the and making it look good.
<source lang="python">
# setup PyMOL for the movie
reinitialize
set matrix_mode, 1
set movie_panel, 1

# load the PDB, make selections for the ligands and
# make the protein look snazzy.
#load /spc/pdb/2jep.pdb
fetch 2jep, asyn=0
remove resn HOH
orient
select l1, c. A and i. 1397
select l2, c. A and i. 1396
select l3, c. B and i. 1396
as cartoon
color grey
show sticks, het
color magnesium, het

# At 30 FPS this is then a 16 second movie.
# We look at the structure for 2 seconds, zoom in to each ligand
# and look at it for another 2 seconds, then, zoom out and look again
# at everything for another 2 seconds.

# initialize the 480 frame movie
mset 1 x480

# zoom all ('scene #1')
frame 1
mview store
# stay here for 2 seconds
frame 60
mview store

# zoom on ligand 1 ('scene #2')
frame 120
zoom l1
mview store
# stay here for 2 seconds
frame 180
mview store

# zoom on ligand 2 ('scene #3')
frame 240
zoom l2
mview store
# stay for 2 seconds
frame 300
mview store

# zoom to ligand 3 ('scene #4')
frame 360
zoom l3
mview store
# stay for 2 seconds
frame 420
mview store

# zoom out ('back to scene #1')
frame 480
zoom
mview store

# interpolate the frames
mview reinterpolate

# play the awesome movie!
mplay

# stop when you want
# mstop
</source>

=== Animating an Alignment ===
<source lang="python">
# setup PyMOL for the movie
reinitialize
set matrix_mode, 1
set movie_panel, 1

# load the PDBs
fetch 1cll 1ggz, async=0

# orient the scene
as cartoon
orient

# make 100-frame movie
mset 1 x100
# goto frame 1
frame 1

# store the camera position and object
# positions in frame 1
mview store
mview store, object=1cll
mview store, object=1ggz

# goto frame 90
frame 90
# align the two proteins
super 1cll, 1ggz
# we rezoom to center the camera on the
# two aligned proteins
zoom
# store the camera positions
mview store
# store the new object position(s)
mview store, object=1cll
mview store, object=1ggz

# have PyMOL stitch together the scenes.
mview reinterpolate
mview reinterpolate, object=1cll
mview reinterpolate, object=1ggz

# rewind
frame 1
# get some popcorn! :-)
mplay
</source>

= See Also =
[[oload]], [[Cealign]], [[find_bind]], [[zero]], [[removeAlt]], [[toGroup]], [[ribbon_width]], [[antialias]], [[cartoon_fancy_helices]], [[depth_cue]], [[ray_trace_fog]], [[ray_opaque_background]], [[defer_builds_mode]], [[ray_trace_mode]].

[[User:Inchoate|Tree]] 19:08, 26 May 2009 (UTC)

User:Inchoate

2009-06-12T22:24:39Z

Warren: /* Terminology */

My name is Jason Vertrees and I'm a postdoc in computational biology. Currently, I study proteins through mathematical models & machine learning. My previous work was in theoretical biophysics.

Also, I am the owner and of the PyMOLWiki website.

If you are interested in Biophysical, Structural or Compuational Biology, check out [http://www.bscb.utmb.edu/ BSCB@UTMB] -- my old school.

'''Jason Vertrees, PhD

''jv(_at-)cs_dot_dartmouth(dot2)edu''

[http://www.cs.dartmouth.edu/~jv/ My Page]

= My ~/.pymolrc =
<source lang="python">
run ~/playground/pymol_scripts/oload.py
run ~/playground/cealign/qkabsch.py
run ~/playground/cealign/cealign.py
run ~/playground/pymol_scripts/find_bind.py
run ~/playground/pymol_scripts/zero.py
run ~/playground/pymol_scripts/removeAlt.py
run ~/playground/pymol_scripts/toGroup.py

one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', \
'GLY':'G', 'PRO':'P', 'CYS':'C'}

set ribbon_width, 8
set antialias,2
set cartoon_fancy_helices,1
set ray_trace_mode,1
set depth_cue,0
set ray_trace_fog,0
set ray_opaque_background,0
set defer_builds_mode, 3
</source>

== To Do ==
* texture_fonts, 1 -- for speed
* pseudo-atoms; you can label them. RightClick->New->PAtom->and then label it; move the atom (and the label goes w/it). You can also move the label by itself
* movie_panel
* mset - clears the movie
* Movie->UpdateMovie
* Scene->Buttons (shows buttons for each scene)
* Scene->Optmize (before saving scenes; use before optimizing)
* Scene->Cache (cache's surface data)
* A good way to make movies seems to be:
** madd
** prepare a scene; turn on scene buttons
** Fn+CTRL+down-arrow # adds the scene;
** madd 1 x90
** mview store, -1
* repeat
* when done do mview reinterpolate
* play the movie
* matrix_mode
* dot_solvent

=== Movie Notes ===
<source lang="python">
#
# Simple movie of independent motions
#

# This create an ala and a tyr. It moves the ala indepdendent
# of the tyr.
#
# Q: Why are the orientations off? What is the equivalent
# command to moving something with mouse_motions?

# reinit
reinitialize

set matrix_mode, 1
# turns on handy scene buttons
set scene_buttons, 1
# turns on the movie panel at the bottom of the sceen
set movie_panel, 1
# turns on a special mouse button panel
config_mouse three_button_motions

# start with an empty movie, scene 1 with 90 frames
mset 1 x90

# create an ala and tyr
frag ala
frag tyr
as spheres

# create our scene
translate [10, 0, 0], object=ala, camera=0
orient

# store the first frame
frame 1
mview store, object=ala

# goto the next frame
frame 45
translate [-20, 0, 0], object=ala, camera=0
orient

# store this frame
mview store, object=ala

#reinterpolate the scene
mview reinterpolate, object=ala
</source>

= Movie Making =
While PyMOL's capability to produce static images is quite powerful, there are some stories that are better told through movies, than static images alone. This little page will provide the necessary ideas, links, code and examples for making movies in PyMOL.

== Your First Movie ==
Movies can be very simple, for example, animating an NMR ensemble:
<source lang="python">
# Your first movie.
fetch 1nmr
mplay

# to stop the movie when you're ready
# type 'mstop'.
</source>

What PyMOL did here was to [[fetch]] the file from the PDB and load it into an object with 20 states. Somewhere between then and issuing [[mplay]] PyMOL created 20 frames for your object and assigned one state to each frame. This created the animated effect as we scroll through the frames.

== Terminology ==
Imagine a complex movie for a moment, a movie that has camera motions, objects moving independently or in concert with other objects, changing colors and representations. To handle camera motions PyMOL must know at all times where the camera is located and what it's pointed toward (as well as clipping planes). For objects to move around or be rotated without regard to the camera (the objects themselves rotate/translate, not just the camera) then PyMOL has to store the coordinates and matrices for these objects, too. Changing colors and representations for each object must somehow also be stored. So, as you can see this is a multidimensional problem: at each time point in your movie, PyMOL must remember positions and representations, as well as make it easy for you to transition between them (interpolation).

Despite these complexities, PyMOL tries to enable movie making for even novice users. Let's start by defining a few PyMOL concepts—states, frames and scenes.

=== Basic Movie Terminology ===
'''object'''
::An object is any PyMOL-object loaded into PyMOL, like atoms, molecules, complexes, etc. When you load an PDB from disk/net it is loaded into PyMOL as an object.
:: [[:Category:Objects|All pages regarding objects]]

'''selection'''
:: A selection is a specifically chosen set of atoms, molecules, complexes etc. in PyMOL. A selection is not an object, it's a subset of stuff from a (collection of) object(s). Selections can be named and when named have are distinguished from objects by having parentheses around their names. For example, ''foo'' would be an object and ''(foo)'' would be some selection. When you pick an atom (and get the default '''(sele)''' selection) or issue the ever-popular [[Select]]ion command, you get a selection.
:: [[:Category:Selections|All pages regarding selections]]

'''states'''
:: A state is a particular conformation (set of coordinates) for a given object. For example an NMR ensemble could contain the same molecule, but in 20 different states. PyMOL can make movies from states. States '''do not store representations''' in PyMOL (eg. cartoons vs. sticks).
:: See also [[:Category:States|All pages regarding states]]

'''scenes'''
'''interpolation'''
:: A scene is the staged representations of objects and the orientation of the camera.
:: See also [[:Category:Scenes|All pages regarding scenes]]

'''frames'''
:: A frame can be thought of as a single frame in a movie reel. A frame stores state information and scene information.
:: See also [[:Category:Frames|All pages regarding frames]]

'''Movie Panel'''
:: The movie panel is a frame indicator strip at the bottom of the screen. It shows a little icon for which frame you're currently on, and whether or not the camera has been set for that frame.
:: See [[movie_panel]] for more information.

== What is a Movie? ==
Now the we have the appropriate terminology to talk about movies in PyMOL, we can discuss what a movie really is. A movie in PyMOL is a series of frames stitched together in some way so as to create the desired animation.

== Movie Making Commands ==
This tutorial assumes you have some basic knowledge about how to use PyMOL (eg. mousing, choosing and setting your representations, etc). If you're not yet at this level, please check out [[:Category:Tutorials|the Tutorial Category]] of pages (most notably the beginner tutorials).

I think it's help to think of the movie as a set of frames, like in a movie reel, so let's start there. (Each command below links to the command's PyMOL wiki page, so feel free to click through for more info.)

=== [[frame]]===
This command tells PyMOL to set the current frame to whichever you desire. To use it, just issue the command, <source lang="python">frame X</source> where '''X''' is some integer number indicating the frame you want to go to. If you issue a frame number greater than the number of frames, PyMOL sets the frame to the highest-numbered frame you have (similarly for negative numbers or numbers smaller than the minimum numbered frame).

Let's try a quick example with [[frame]],
<source lang="python">
# create an empty 90 frame movie
mset 1 x90
# turn on the movie panel (bottom of screen)
set movie_panel, on
# goto frame one
frame 1
# try some intermediate frames; notice the blue indicator in the movie panel
frame 10
frame 50
frame 90
# try going beyond the end and see what PyMOL does
frame -1
frame 100
# play through the empty movie
mplay
# stop the movie
mstop
</source>

=== [[States|set state]] ===
Again, states are particular stored conformations of objects. Here we use PyMOL to set and get the states, and see how PyMOL mapped them to our earlier movie example.

This command has a similar idea of [[frame]], but works a little differently. Instead of typing,
<source lang="python">
# invalid command
state 40
</source>
in PyMOL we [[set]] the [[States|state]]:
<source lang="python">
# how to set a state in PyMOL
set state, stateNo, objectName

# for example
# set state to 40
set state, 40

# also, get state
get state
</source>

==== States & Frames (optional reading) ====
As an example, look at the code from the "first movie":
<source lang="python">
fetch 1nmr
mplay
# issue mstop, to stop the movie
</source>

We can do a couple things now, let's try counting the number of states and frames PyMOL now knows about:
<source lang="python">
# how many frames does PyMOL know about?
count_frames

# what about states?
count_states
</source>

and now let's see how PyMOL mapped frames to states. Using the above commands and a little Python, let's see how PyMOL mapped the frames to states:
<source lang="python">
python
for x in range(1,cmd.count_frames()+1):
cmd.frame(x)
print "Frame => %s; and State => %s" % ( str(x), str(cmd.get('state')))
python end
</source>
which should show a 1-1 mapping of states to frames.

=== [[mset]] ===
[[mset]] is a very powerful command. This command tells PyMOL how to assign states to frames. So, now you see why it's necessary to clearly distinguish between and use the two. Let's learn how to use [[mset]].

The syntax for [[mset]] can be a little tricky at first. I would write the syntax as:
<source lang="python">
mset stateSpec frameSpec
</source>
which assigns the states in '''stateSpec''' to the frames in '''frameSpec'''., where '''stateSpec''' is any mset-valid state specification. PyMOl supports to patterns for '''stateSpec'''. You can do simply supply a number eg
<source lang="python">
mset 1
</source>
or you can specify a range of states—like 1 through 55 as
<source lang="python">
# setting states 1 through 55
# caution: notice the space: 1 -55, not 1-55 (this is a PyMOL parser caveat)
mset 1 -55
</source>
Simple enough. Now for '''frameSpec''' you can specify a single frame number like so or you can specify ''how many frames PyMOL should use to map to your specified states'' with the '''xNumber'' command. This will make sense with an example
<source lang="python">
# Recall: mset stateSpec frameSpec
# so we are setting STATE 1 across a span of 90 frames
mset 1 x90

# Recall: mset stateSpec frameSpec
# so we are setting states 1..120 to the next 120 frames
mset 1 -120 x120
</source>

NB: Actually the syntax is a little more complicated than this as PyMOL's mset command has the ability to remember in which frame the prior specification left the movie. So, you can sort of chain the specifications. Type ''help mset'' in PyMOL for more info or see [[mset]].

=== [[mview]] ===
The [[mview]] command can be intimidating, but all we need to know about it at present is that it can store the (1) camera position or (2) a given object position. The idea is to essentially make 'way points' in your movie and have PyMOL interpolate the in-between positions/coordinates, etc. For example, if I wanted to make a 100-frame movie of a zoom into an object, I could store and manually set 100 camera positions, or I could do the starting position and the final position and ask PyMOL to just interpolate that over 100 frames. The latter idea is obviously much simpler. So simple in fact, let's make a super-quick movie that does exactly what I just mentioned—100 frames of a slow zoom into some object. Start with a fresh PyMOL session ([[reinitialize]]) and then copy/paste the following:
<source lang="python" line=1>
# let's initialize the movie to 100 frames, all of state 1
# it's ONLY state 1, because we're only moving the camera around, not
# changing structure coordinates of the leucine:
mset 1 x100

# show a leucine
frag leu

# position the residue
orient

# let's store the current camera position
mview store

# now set our way point to be frame 100
frame 100

# now let's zoom into some atom on the fragment
zoom ID 10

# now save this view at frame 100
mview store

# last thing is to tell PyMOL to interpolate the 100 frame zoom
# so we don't have to do those 100 snapshots:
mview reinterpolate

# voila, you have a movie. To watch it go back to frame 1 and play it
frame 1
mplay

# mstop when you're ready
</source>

'But, hold on!' you might say. Why is it so herky-jerky? We have smooth zooming but then a snap and back to frame one! Well, we never gave PyMOL any number of frames to interpolate the change from frame 100 back to frame 1 (since it wraps). If we wanted an a '''zoom in''' that was equally as fast as the '''zoom out''' we would simply '''replace line #16''' with
<source lang="python">
# now set our way point to be frame 100
frame 100
</source>
but, if we wanted a slow, zoom in and a ''fast'' zoom out we could do
<source lang="python">
# now set our way point to be frame 100
frame 80
</source>
instead which would only give PyMOL 20 frames with which to zoom us out. Try it!

==== Very Basic Mview Syntax ====
''This is a simple overview, see [[mview]] for complete details.''

Using [[mview]] as you can see from above is pretty simple. The very basic syntax is:
<source lang="python">
# store the camera OR some object given by objName (if it's supplied)
mview store[, object=objName]

# reinterpolate (link together the positions) for the saved camera or object
mview reinterpolate[, object=objName]
</source>
If you leave off the '''object=objName''' then you're storing the '''camera information only'''—and so none of your objects will be moving anywhere—just the camera. If you include an object name, then it stores that object's position information in the current frame. The '''mview store''' tells PyMOL to store the camera or objects coordinates, while the '''mview reinterpolate''' command tells PyMOL to link together the saved positions for the camera or the selected object in a smooth, cool way.

== Simple Movie Examples ==
We now the ability to make some pretty simple, but cool movies. So, let's try a few.

=== Multiple Zooming ===
Let's try making a movie where we zoom into each ligand that's not water. In order to make this movie, I had to find a protein with suitable ligands, so you can do the same for your own protein. Just replace the hard-coded residue numbers.

'''Goal:''' Make a movie that zoom into the three ligands, stays on that ligand for 2 seconds, then moves to the next. I also want smooth zoom out at the end. Don't let the length of this movie script throw you off, you've seen all of the movie commands and the initial commands are just loading the and making it look good.
<source lang="python">
# setup PyMOL for the movie
reinitialize
set matrix_mode, 1
set movie_panel, 1

# load the PDB, make selections for the ligands and
# make the protein look snazzy.
#load /spc/pdb/2jep.pdb
fetch 2jep, asyn=0
remove resn HOH
orient
select l1, c. A and i. 1397
select l2, c. A and i. 1396
select l3, c. B and i. 1396
as cartoon
color grey
show sticks, het
color magnesium, het

# At 30 FPS this is then a 16 second movie.
# We look at the structure for 2 seconds, zoom in to each ligand
# and look at it for another 2 seconds, then, zoom out and look again
# at everything for another 2 seconds.

# initialize the 480 frame movie
mset 1 x480

# zoom all ('scene #1')
frame 1
mview store
# stay here for 2 seconds
frame 60
mview store

# zoom on ligand 1 ('scene #2')
frame 120
zoom l1
mview store
# stay here for 2 seconds
frame 180
mview store

# zoom on ligand 2 ('scene #3')
frame 240
zoom l2
mview store
# stay for 2 seconds
frame 300
mview store

# zoom to ligand 3 ('scene #4')
frame 360
zoom l3
mview store
# stay for 2 seconds
frame 420
mview store

# zoom out ('back to scene #1')
frame 480
zoom
mview store

# interpolate the frames
mview reinterpolate

# play the awesome movie!
mplay

# stop when you want
# mstop
</source>

=== Animating an Alignment ===
<source lang="python">
# setup PyMOL for the movie
reinitialize
set matrix_mode, 1
set movie_panel, 1

# load the PDBs
fetch 1cll 1ggz, async=0

# orient the scene
as cartoon
orient

# make 100-frame movie
mset 1 x100
# goto frame 1
frame 1

# store the camera position and object
# positions in frame 1
mview store
mview store, object=1cll
mview store, object=1ggz

# goto frame 90
frame 90
# align the two proteins
super 1cll, 1ggz
# we rezoom to center the camera on the
# two aligned proteins
zoom
# store the camera positions
mview store
# store the new object position(s)
mview store, object=1cll
mview store, object=1ggz

# have PyMOL stitch together the scenes.
mview reinterpolate
mview reinterpolate, object=1cll
mview reinterpolate, object=1ggz

# rewind
frame 1
# get some popcorn! :-)
mplay
</source>

= See Also =
[[oload]], [[Cealign]], [[find_bind]], [[zero]], [[removeAlt]], [[toGroup]], [[ribbon_width]], [[antialias]], [[cartoon_fancy_helices]], [[depth_cue]], [[ray_trace_fog]], [[ray_opaque_background]], [[defer_builds_mode]], [[ray_trace_mode]].

[[User:Inchoate|Tree]] 19:08, 26 May 2009 (UTC)

Zero residues

2009-05-12T17:10:09Z

Warren: /* CODE */

== OVERVIEW ==
This script will renumber all the residues such that the first one is numbered 0. This is often helpful when dealing with alignments.

=== Ordering from Sequence End ===
If you want to change numbering based off the last residue's number in the sequence, just replace '''first''' in the code with '''last'''.

== EXAMPLE ==
<source lang="python">
zero_residues 1AFK
zero_residues *

# make the first residue's number, 30.
zero_residues 1AFK, 30
</source>

== INSTALL ==
Copy the source code below, to "zero_residues.py" and then simply run the file. The command, "zero_residues" will now be defined and can be used as in the examples above.

== CODE ==
<source lang="python">
import pymol

def zero_residues(sel1,offset=0):
"""
PURPOSE: renumbers the residues so that the first one is zero, or offset .
USAGE: zero_residues protName # first residue is 0
USAGE: zero_residues protName, 5 # first residue is 5
EXAMPLE: zero_residues *
"""
offset = int(offset)

# variable to store the offset
stored.first = None
# get the names of the proteins in the selection
names = cmd.get_names(selection=sel1)

# for each name shown
for p in names:
# get this offset
cmd.iterate("first %s and polymer and n. CA" % p,"stored.first=resi")
# don't waste time if we don't have to
if ( stored.first == offset ):
continue;
# reassign the residue numbers
cmd.alter("%s" % p, "resi=str(int(resi)-%s)" % str(int(stored.first)-offset))
# update pymol
cmd.sort()

# let pymol know about the function
cmd.extend("zero_residues", zero_residues)
</source>

[[Category:Script_Library|Zero Residues]]
[[Category:ObjSel_Scripts]]

Linux Install

2009-03-18T20:27:56Z

Warren: /* External Links to Distribution-specific Package Information */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng

== Generic Linux ==

=== Quick Install for Latest Features ===
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.

This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access. It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it. This should install PyMOL onto your system so that any users on your system can use it. To easily get the latest version, do the following:
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.

=== From Source ===
The following instructions require you to be root.

* Under modern Linux, you will need the dependencies installed first.
** Fedora 9: <source lang="text">yum install python-devel tkinter libpng-devel freeglut-devel freetype-devel</source>
* To obtain a copy of the current source code <source lang="bash">svn https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-src</source>
* Then go into the source directory ('''pymol-src'''). <source lang="bash">cd pymol-src</source>
* Run the first stage of the installation <source lang="python">python setup.py install</source>
* Run the second stage of the installation <source lang="python">python setup2.py install</source> A launch script "pymol" will have been created.
* Test the install <source lang="python">./pymol</source> If you get an error message "ImportError: No module named Pmw" and lack half of the user interface, then run the additional command <source lang="python">python setup2.py install pmw</source> to install a copy of the Python MegaWidgets.
* You may now wish to copy the executable to a suitable location <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>

To uninstall pymol built from source <source lang="bash">python setup2.py uninstall</source>

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
* tcl-8_4_11.tgz
* tk-8_4_11.tgz
* zlib-1_2_3.tgz
* libpng-1_2_8.tgz
* python-2_4_2.tgz
* numeric-24_2.tgz
* pmw-1_2.tgz
* freetype-2_1_10.tgz
--and--
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)

====Supported Packages====
The above packages don't need to be installed from their source-packages only. That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages. '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages. PyMOL needs the source/header files to compile against. For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL. Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>

==== Installing a Script Without Superuser Access ====
Install the script following the instructions by the distributor. Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).

== External Links to Distribution-specific Packages ==

Some of the detailed information in the subsequent sections may be obsolete, so here are links to package information pages:

* Fedora: [https://admin.fedoraproject.org/pkgdb/packages/name/pymol]

* RHEL: [https://fedoraproject.org/wiki/SIGs/SciTech/PackageList]

* Ubuntu: [http://packages.ubuntu.com/jaunty/science/pymol]

* Debian: [http://packages.debian.org/lenny/pymol]

* OpenSUSE: [http://software.opensuse.org/search?p=1&q=pymol]

* Gentoo-portage: [http://gentoo-portage.com/sci-chemistry/pymol]

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]

A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
layman -a dberkholz && emerge =sci-chemistry/pymol-9999

There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
svn co http://svn.olausson.de/molmod/trunk
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.

All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:

<pre>
Driver "nvidia"
</pre>

Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.

<pre>
Section "Extensions"
Option "Composite" "Disable"
EndSection
</pre>

In Section "Screen" add the following line to enable quad-buffered stereo:

<pre>Option "Stereo" "3"</pre>

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL. ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a

# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Linux Install

2009-03-18T20:26:52Z

Warren:

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng

== Generic Linux ==

=== Quick Install for Latest Features ===
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.

This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access. It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it. This should install PyMOL onto your system so that any users on your system can use it. To easily get the latest version, do the following:
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.

=== From Source ===
The following instructions require you to be root.

* Under modern Linux, you will need the dependencies installed first.
** Fedora 9: <source lang="text">yum install python-devel tkinter libpng-devel freeglut-devel freetype-devel</source>
* To obtain a copy of the current source code <source lang="bash">svn https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-src</source>
* Then go into the source directory ('''pymol-src'''). <source lang="bash">cd pymol-src</source>
* Run the first stage of the installation <source lang="python">python setup.py install</source>
* Run the second stage of the installation <source lang="python">python setup2.py install</source> A launch script "pymol" will have been created.
* Test the install <source lang="python">./pymol</source> If you get an error message "ImportError: No module named Pmw" and lack half of the user interface, then run the additional command <source lang="python">python setup2.py install pmw</source> to install a copy of the Python MegaWidgets.
* You may now wish to copy the executable to a suitable location <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>

To uninstall pymol built from source <source lang="bash">python setup2.py uninstall</source>

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
* tcl-8_4_11.tgz
* tk-8_4_11.tgz
* zlib-1_2_3.tgz
* libpng-1_2_8.tgz
* python-2_4_2.tgz
* numeric-24_2.tgz
* pmw-1_2.tgz
* freetype-2_1_10.tgz
--and--
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)

====Supported Packages====
The above packages don't need to be installed from their source-packages only. That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages. '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages. PyMOL needs the source/header files to compile against. For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL. Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>

==== Installing a Script Without Superuser Access ====
Install the script following the instructions by the distributor. Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).

== External Links to Distribution-specific Package Information ==

Some of the detailed information in the subsequent sections may be obsolete, so here are links to package information pages:

* Fedora: [https://admin.fedoraproject.org/pkgdb/packages/name/pymol]

* RHEL: [https://fedoraproject.org/wiki/SIGs/SciTech/PackageList]

* Ubuntu: [http://packages.ubuntu.com/jaunty/science/pymol]

* Debian: [http://packages.debian.org/lenny/pymol]

* OpenSUSE: [http://software.opensuse.org/search?p=1&q=pymol]

* Gentoo-portage: [http://gentoo-portage.com/sci-chemistry/pymol]

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]

A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
layman -a dberkholz && emerge =sci-chemistry/pymol-9999

There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
svn co http://svn.olausson.de/molmod/trunk
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.

All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:

<pre>
Driver "nvidia"
</pre>

Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.

<pre>
Section "Extensions"
Option "Composite" "Disable"
EndSection
</pre>

In Section "Screen" add the following line to enable quad-buffered stereo:

<pre>Option "Stereo" "3"</pre>

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL. ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a

# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Stereo 3D Display Options

2009-02-12T02:26:54Z

Warren: /* Passive Stereo 3D Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and fuzzy for desktop use. Also, a band of about 20 pixels around on the edge of the display are invisible, and this limitation cannot be eliminated through overscan since the image must be scanned at native resolution in order to support stereo 3D. The workaround is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.

Aside from the above concerns, the quality of the DLP stereo 3D effect is exceptional: there is absolutely no ghosting or cross-talk between the two images.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - not yet tested, but are expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== One Piece Multi-layer LCD Displays ===

Affordable!

* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Great stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo mode, but even so, this 650 USD display provides excellent 3D molecular visualization in both full-screen in windowed modes. - WLD ('''The Zalman ZM-M220W is DeLano Scientific's RECOMMENDED SOLUTION as of Feb 11, 2009!''').
* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD

=== Mirror-based Multi-LCD Solutions ===

Expensive!

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T18:03:58Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and fuzzy for desktop use. Also, a band of about 20 pixels around on the edge of the display are invisible, and this limitation cannot be eliminated through overscan since the image must be scanned at native resolution in order to support stereo 3D. The workaround is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.

Aside from the above concerns, the quality of the DLP stereo 3D effect is exceptional: there is absolutely no ghosting or cross-talk between the two images.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - not yet tested, but are expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T17:42:43Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and fuzzy for desktop use. Also, pixels around on the edge of the display are invisible, and this limitation cannot be worked around through overscan since the image must be scanned at 100% in order to support the stereo 3D mode. The solution is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.

Aside from the above concerns, the quality of the DLP stereo 3D effect is exceptional: there is absolutely no ghosting or cross-talk between the two images.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - not yet tested, but are expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T17:40:10Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and fuzzy for desktop use. Also, pixels around on the edge of the display are invisible, and this limitation cannot be worked around through overscan since the image must be scanned at 100% in order to support the stereo 3D mode. The solution is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.

Aside from the above concerns, the quality of the DLP stereo 3D effect is exceptional: there is absolutely zero ghosting and no cross-talk between the two images.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - not yet tested, but are expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:38:23Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use. Also, pixels around on the edge of the display are invisible, and this limitation cannot be worked around through overscan since the image must be scanned at 100% in order to support the stereo 3D mode. The solution is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - not yet tested, but are expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:38:14Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use. Also, pixels around on the edge of the display are invisible, and this limitation cannot be worked around through overscan since the image must be scanned at 100% in order to support the stereo 3D mode. The solution is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - not yet tested but are expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:37:40Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use. Also, pixels around on the edge of the display are invisible, and this limitation cannot be worked around through overscan since the image must be scanned at 100% in order to support the stereo 3D mode. The solution is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:34:19Z

Warren: /* Autostereoscopic LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use. Also, pixels around on the edge of the display are invisible, and this limitation cannot be worked around through compression since the image must be scanned at 100% in order to support the stereo 3D mode.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:18:52Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use. Also, pixels around on the edge of the display are invisible, and this limitation cannot be worked around through compression since the image must be scanned at 100% in order to support the stereo 3D mode.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

* [http://www.mitsubishi-tv.com/ Mitsubishi 3D-Ready DLP HDTVs] - expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD

See [http://www.3dmovielist.com/3dhdtvs.html The 3D HDTV List] for more 3D-capable HDTV options.

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:11:18Z

Warren: /* One Piece Multi-layer LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - Work with PyMOL 1.2b3 & later without any special drivers. 3D HTDVs are not as useful as 3D LCDs because you lost about 15 pixels around the edge of the display. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:10:24Z

Warren: /* One Piece Multi-layer LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - Work with PyMOL 1.2b3 & later without any special drivers. 3D HTDVs are not as useful as 3D LCDs because you lost about 15 pixels around the edge of the display. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later without any special drivers. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:09:27Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - Work with PyMOL 1.2b3 & later without any special drivers. 3D HTDVs are not as useful as 3D LCDs because you lost about 15 pixels around the edge of the display. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later. However, this display exhibits far too much cross-talk between the two stereo images -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:09:18Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - Works with PyMOL 1.2b3 & later without any special drivers. 3D HTDVs are not as useful as 3D LCDs because you lost about 15 pixels around the edge of the display. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later. However, this display exhibits far too much cross-talk between the two stereo images -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-08T16:07:28Z

Warren: /* One Piece Multi-layer LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - Quadro driver support still lacking as of Feb. 1st, 2009 - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - works with PyMOL 1.2b3 & later. However, this display exhibits far too much cross-talk between the two stereo images -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - works with PyMOL 1.2b3 & later. Excellent stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-04T23:53:03Z

Warren: /* One Piece Multi-layer LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - Quadro driver support still lacking as of Feb. 1st, 2009 - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - being tested as of Feb 1st, 2009, but so far, this display exhibits far too much cross-talk between the two images. -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - now works "OUT OF THE BOX" with PyMOL 1.2b3 & later (issue "stereo byrow"). Excellent stereo quality provided that all drawn lines aare at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-04T23:52:19Z

Warren: /* One Piece Multi-layer LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - Quadro driver support still lacking as of Feb. 1st, 2009 - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - being tested as of Feb 1st, 2009, but so far, this display exhibits far too much cross-talk between the two images. -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - NOW WORKS "out of the box" with PyMOL 1.2b3 and later with "stereo byrow". Excellent stereo quality provided that all drawn lines aare at least 2 pixels thick. Menus are a bit awkward to use while in stereo, however, this 600 USD display provides excellent molecular visualization in both full-screen in windowed modes. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T23:22:37Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - Quadro driver support still lacking as of Feb. 1st, 2009 - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - being tested as of Feb 1st, 2009, but so far, this display exhibits far too much cross-talk between the two images. -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - unsuitable for PyMOL because the vertical resolution is halved. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T23:22:12Z

Warren: /* Categories */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - as of Feb. 1st, 2009, Quadro driver support still lacking - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - being tested as of Feb 1st, 2009, but so far, this display exhibits far too much cross-talk between the two images. -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - unsuitable for PyMOL because the vertical resolution is halved. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T23:21:15Z

Warren: /* Autostereoscopic LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - as of Feb. 1st, 2009, Quadro driver support still lacking - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - being tested as of Feb 1st, 2009, but so far, this display exhibits far too much cross-talk between the two images. -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - unsuitable for PyMOL because the vertical resolution is halved. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T23:20:52Z

Warren: /* One Piece Multi-layer LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - as of Feb. 1st, 2009, Quadro driver support still lacking - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - being tested as of Feb 1st, 2009, but so far, this display exhibits far too much cross-talk between the two images. -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - unsuitable for PyMOL because the vertical resolution is halved. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical display resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T22:37:09Z

Warren: /* One Piece Multi-layer LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - as of Feb. 1st, 2009, Quadro driver support still lacking - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D] - currently being tested as of Feb 1st, 2009, but so far, this display exhibits far too much cross-talk between the right and left-hand images. -WLD
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - unsuitable for PyMOL because the vertical resolution is halved. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical display resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T22:07:57Z

Warren: /* LCD Displays (120 Hz) */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacking Quadro driver support as of Feb 1st, 2009 - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - as of Feb. 1st, 2009, Quadro driver support still lacking - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D]
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - unsuitable for PyMOL because the vertical resolution is halved. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical display resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T22:07:02Z

Warren: /* Autostereoscopic LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but as of Feb 1st, still lacks mandatory Quadro driver support from nVidia. - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - as of Feb. 1st, 2009, Quadro driver support still lacking - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D]
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - unsuitable for PyMOL because the vertical resolution is halved. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies] - apparently unsuitable for PyMOL because vertical display resolution is halved.
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T22:06:09Z

Warren: /* One Piece Multi-layer LCD Displays */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but as of Feb 1st, still lacks mandatory Quadro driver support from nVidia. - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - as of Feb. 1st, 2009, Quadro driver support still lacking - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D]
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor] - unsuitable for PyMOL because the vertical resolution is halved. - WLD

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T22:05:35Z

Warren: /* DLP Projection Televisions */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but as of Feb 1st, still lacks mandatory Quadro driver support from nVidia. - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs] - as of Feb. 1st, 2009, Quadro driver support still lacking - WLD

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D]
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor]

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T22:04:54Z

Warren: /* LCD Displays (120 Hz) */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but as of Feb 1st, still lacks mandatory Quadro driver support from nVidia. - WLD

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs]

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D]
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor]

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Stereo 3D Display Options

2009-02-01T22:04:21Z

Warren: /* LCD Displays (120 Hz) */

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world!

== Categories ==

* '''[[#Active_Stereo_3D|Active Stereo 3D]]''' -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
* '''[[#Passive_Stereo_3D|Passive Stereo 3D]]''' -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a few people.
* '''[[#Autostereoscopic_3D|Autostereoscopic 3D]]''' -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.

== Active Stereo 3D (High-Refresh) Displays ==

This solution would be analogous to using desktop CRT monitors with shutter glasses.

=== LCD Displays (120 Hz)===

Are any of these displays on the market yet?

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] - Not yet on the market as of Feb 1st, 2009 - WLD

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market, but still lacks Quadro driver support from nVidia.

=== DLP Projection Televisions ===

Projection televisions tend to be too large and blurry for desktop use.

* [http://pages.samsung.com/us/dlp3d Samsung 3D-Ready DLP HDTVs]

== Passive Stereo 3D Displays ==

=== Mirror-based Multi-LCD Solutions ===

* [http://www.planar3d.com Planar3D] "I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!" - WLD.
* [http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3 Omnia MIMO]

=== One Piece Multi-layer LCD Displays ===

* [http://www.iz3d.com IZ3D]
* [http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 Zalman 22-inch 3D LCD monitor]

== Autostereoscopic LCD Displays ==

Some autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.

* [http://www.dti3d.com Dimension Technologies Inc.]
* [http://www.seereal.com SeeReal Technologies]
* [http://www.newsight.com/3d-products/displays.html NewSight Corp.]

== Stereo 3D Projectors ==

Although these displays require shutter glasses out of the box, when combined with the adapters below and a special "silvered" screen, they can be used to project Passive Stereo 3D to a large audience.

=== Active Stereo 3D DLP Projectors ===

* [http://www.depthq.com DepthQ Stereoscopic] "The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products." - WLD.
* [http://www.christiedigital.com/AMEN/Products/christieMirageS4K.htm Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR] "I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card." - WLD.

=== Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors ===

These devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.

* [http://reald-corporate.com/scientific/projectorzscreen.asp RealD StereoGraphics Projection ZScreen]

== Who Says What? ==

If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.

* WLD = Warren L. DeLano of DeLano Scientific LLC

[[Category:Hardware_Options]]

Linux Install

2008-10-28T22:32:40Z

Warren: /* From Source */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng

== Generic Linux ==

=== Quick Install for Latest Features ===
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.

This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access. It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it. This should install PyMOL onto your system so that any users on your system can use it. To easily get the latest version, do the following:
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.

=== From Source ===
The following instructions require you to be root.

* Under modern Linux, you will need the dependencies installed first.
** Fedora 9: <source lang="text">yum install python-devel tkinter libpng-devel freeglut-devel freetype-devel</source>
* To obtain a copy of the current source code <source lang="bash">svn https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-src</source>
* Then go into the source directory ('''pymol-src'''). <source lang="bash">cd pymol-src</source>
* Run the first stage of the installation <source lang="python">python setup.py install</source>
* Run the second stage of the installation <source lang="python">python setup2.py install</source> A launch script "pymol" will have been created.
* Test the install <source lang="python">./pymol</source> If you get an error message "ImportError: No module named Pmw" and lack half of the user interface, then run the additional command <source lang="python">python setup2.py install pmw</source> to install a copy of the Python MegaWidgets.
* You may now wish to copy the executable to a suitable location <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>

To uninstall pymol built from source <source lang="bash">python setup2.py uninstall</source>

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
* tcl-8_4_11.tgz
* tk-8_4_11.tgz
* zlib-1_2_3.tgz
* libpng-1_2_8.tgz
* python-2_4_2.tgz
* numeric-24_2.tgz
* pmw-1_2.tgz
* freetype-2_1_10.tgz
--and--
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)

====Supported Packages====
The above packages don't need to be installed from their source-packages only. That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages. '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages. PyMOL needs the source/header files to compile against. For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL. Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>

==== Installing a Script Without Superuser Access ====
Install the script following the instructions by the distributor. Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]

A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
layman -a dberkholz && emerge =sci-chemistry/pymol-9999

There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
svn co http://svn.olausson.de/molmod/trunk
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.

All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:

<pre>
Driver "nvidia"
</pre>

Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.

<pre>
Section "Extensions"
Option "Composite" "Disable"
EndSection
</pre>

In Section "Screen" add the following line to enable quad-buffered stereo:

<pre>Option "Stereo" "3"</pre>

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL. ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a

# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Linux Install

2008-10-28T22:31:54Z

Warren: /* From Source */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng

== Generic Linux ==

=== Quick Install for Latest Features ===
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.

This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access. It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it. This should install PyMOL onto your system so that any users on your system can use it. To easily get the latest version, do the following:
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.

=== From Source ===
The following instructions require you to be root.

* Under modern Linux, you will need the dependencies installed first.
** Fedora 9: <source lang="text">yum install python-devel tkinter libpng-devel freeglut-devel freetype-devel</source>
* To obtain a copy of the current source code <source lang="bash">svn https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-src</source>
* Then go into the source directory ('''pymol-src'''). <source lang="bash">cd pymol-src</source>
* Run the first stage of the installation <source lang="python">python setup.py install</source>
* Run the second stage of the installation <source lang="python">python setup2.py install</source> A launch script "pymol" will have been created.
* Test the install <source lang="python">./pymol</source> If you get an error message "ImportError: No module named Pmw" and are missing half of the user interface, then run the additional command <source lang="python">python setup2.py install pmw</source> to install a copy of the Python MegaWidgets.
* You may now wish to copy the executable to a suitable location <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>

To uninstall pymol built from source <source lang="bash">python setup2.py uninstall</source>

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
* tcl-8_4_11.tgz
* tk-8_4_11.tgz
* zlib-1_2_3.tgz
* libpng-1_2_8.tgz
* python-2_4_2.tgz
* numeric-24_2.tgz
* pmw-1_2.tgz
* freetype-2_1_10.tgz
--and--
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)

====Supported Packages====
The above packages don't need to be installed from their source-packages only. That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages. '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages. PyMOL needs the source/header files to compile against. For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL. Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>

==== Installing a Script Without Superuser Access ====
Install the script following the instructions by the distributor. Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]

A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
layman -a dberkholz && emerge =sci-chemistry/pymol-9999

There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
svn co http://svn.olausson.de/molmod/trunk
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.

All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:

<pre>
Driver "nvidia"
</pre>

Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.

<pre>
Section "Extensions"
Option "Composite" "Disable"
EndSection
</pre>

In Section "Screen" add the following line to enable quad-buffered stereo:

<pre>Option "Stereo" "3"</pre>

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL. ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a

# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Linux Install

2008-10-28T22:08:36Z

Warren:

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng

== Generic Linux ==

=== Quick Install for Latest Features ===
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.

This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access. It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it. This should install PyMOL onto your system so that any users on your system can use it. To easily get the latest version, do the following:
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.

=== From Source ===
* Under modern Linux, you will need the dependencies installed first (requires root).
** <source lang="python">Fedora9% yum install python-devel tkinter libpng-devel freeglut-devel freetype-devel</source>
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
* tcl-8_4_11.tgz
* tk-8_4_11.tgz
* zlib-1_2_3.tgz
* libpng-1_2_8.tgz
* python-2_4_2.tgz
* numeric-24_2.tgz
* pmw-1_2.tgz
* freetype-2_1_10.tgz
--and--
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)

====Supported Packages====
The above packages don't need to be installed from their source-packages only. That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages. '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages. PyMOL needs the source/header files to compile against. For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL. Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>

==== Installing a Script Without Superuser Access ====
Install the script following the instructions by the distributor. Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]

A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
layman -a dberkholz && emerge =sci-chemistry/pymol-9999

There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
svn co http://svn.olausson.de/molmod/trunk
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.

All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:

<pre>
Driver "nvidia"
</pre>

Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.

<pre>
Section "Extensions"
Option "Composite" "Disable"
EndSection
</pre>

In Section "Screen" add the following line to enable quad-buffered stereo:

<pre>Option "Stereo" "3"</pre>

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL. ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a

# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Linux Install

2008-10-28T21:54:52Z

Warren: /* From Source */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng

== Generic Linux ==

=== Quick Install for Latest Features ===
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.

This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access. It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it. This should install PyMOL onto your system so that any users on your system can use it. To easily get the latest version, do the following:
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.

=== From Source ===
* Assuming that you're running under Linux, you'll need the following dependencies installed first:
python-devel, libpng-devel,
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
* tcl-8_4_11.tgz
* tk-8_4_11.tgz
* zlib-1_2_3.tgz
* libpng-1_2_8.tgz
* python-2_4_2.tgz
* numeric-24_2.tgz
* pmw-1_2.tgz
* freetype-2_1_10.tgz
--and--
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)

====Supported Packages====
The above packages don't need to be installed from their source-packages only. That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages. '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages. PyMOL needs the source/header files to compile against. For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL. Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>

==== Installing a Script Without Superuser Access ====
Install the script following the instructions by the distributor. Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]

A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
layman -a dberkholz && emerge =sci-chemistry/pymol-9999

There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
svn co http://svn.olausson.de/molmod/trunk
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.

All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:

<pre>
Driver "nvidia"
</pre>

Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.

<pre>
Section "Extensions"
Option "Composite" "Disable"
EndSection
</pre>

In Section "Screen" add the following line to enable quad-buffered stereo:

<pre>Option "Stereo" "3"</pre>

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL. ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a

# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Linux Install

2008-10-28T21:50:29Z

Warren: /* From Source */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng

== Generic Linux ==

=== Quick Install for Latest Features ===
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.

This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access. It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it. This should install PyMOL onto your system so that any users on your system can use it. To easily get the latest version, do the following:
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
* tcl-8_4_11.tgz
* tk-8_4_11.tgz
* zlib-1_2_3.tgz
* libpng-1_2_8.tgz
* python-2_4_2.tgz
* numeric-24_2.tgz
* pmw-1_2.tgz
* freetype-2_1_10.tgz
--and--
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)

====Supported Packages====
The above packages don't need to be installed from their source-packages only. That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages. '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages. PyMOL needs the source/header files to compile against. For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL. Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>

==== Installing a Script Without Superuser Access ====
Install the script following the instructions by the distributor. Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]

A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
layman -a dberkholz && emerge =sci-chemistry/pymol-9999

There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
svn co http://svn.olausson.de/molmod/trunk
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.

All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:

<pre>
Driver "nvidia"
</pre>

Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.

<pre>
Section "Extensions"
Option "Composite" "Disable"
EndSection
</pre>

In Section "Screen" add the following line to enable quad-buffered stereo:

<pre>Option "Stereo" "3"</pre>

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL. ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a

# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Linux Install

2008-10-28T21:49:54Z

Warren: /* 0.99rc1 note! */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])
* libpng

== Generic Linux ==

=== Quick Install for Latest Features ===
Many people want the latest versions of PyMOL as they usually have valuable features, but don't want to build PyMOL. Building PyMOL is generally '''very''' simple.

This quick install assumes you already have a [http://subversion.tigris.org/ Subversion] client installed, have some sort of superuser (root) access, and have internet access. It will download the most current version from [http://pymol.sf.net PyMOL's Projet Page] and install it. This should install PyMOL onto your system so that any users on your system can use it. To easily get the latest version, do the following:
<source lang="python">
mkdir pymol_temp
cd pymol_temp
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
cd pymol
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin/pymol
</source>
Now, just remove the '''pymol_temp''' directory if you want and you're done.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. The '''ext''' package is available from the Source Forge download section and contains all the necessary software to make PyMol run. In the most recent available version (0.99rc1) this includes
* tcl-8_4_11.tgz
* tk-8_4_11.tgz
* zlib-1_2_3.tgz
* libpng-1_2_8.tgz
* python-2_4_2.tgz
* numeric-24_2.tgz
* pmw-1_2.tgz
* freetype-2_1_10.tgz
--and--
* (freeglut-2_4_0.tgz
--or--
* glut-3_7_6.tgz)

====Supported Packages====
The above packages don't need to be installed from their source-packages only. That is, you can use your system's installer (eg. yum, YaST, apt-get, rpm, etc.) to install the packages. '''Just be sure, if you install the above packages with your system's installer, that you also include the development packages. PyMOL needs the source/header files to compile against. For example, don't only install, ''freeglut-2.4.0'' but also look for, and install, ''freeglut-2.4.-devel'' '''.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

==== Installing without Superuser (root) Privileges ====
Use the prefix command to specify where to install PyMOL. Then, you'll need to modify your '''PYTHONPATH''' variable,
<source lang="bash" line="1">
# install to prefix
python setup.py install --prefix /dir_to/pymol/py_build
# update your PYTHONPATH variable
export PYTHONPATH=$PYTHONPATH:/dir_to/pymol/py_build/lib/python{version}/site-packages
# install to prefix (this step _is_ needed)
python setup2.py install --prefix /dir_to/pymol/py_build
# now you can run PyMOL
./pymol
</source>

==== Installing a Script Without Superuser Access ====
Install the script following the instructions by the distributor. Then, add the path where the module was built to the PYTHONPATH environment variable (if needed).

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions in portage [http://www.gentoo-portage.com/sci-chemistry/pymol pymol for gentoo]

A version of the latest svn build is avaible via the dberkholz overlay, which can be used with
layman -a dberkholz && emerge =sci-chemistry/pymol-9999

There is ongoing development in providing plugins via ebuilds with an thread in [http://bugs.gentoo.org/show_bug.cgi?id=209970 gentoo bugzilla]. The ebuild can be checked out via svn
svn co http://svn.olausson.de/molmod/trunk
There is also svn ebuild of pymol, which contains all bugfixes which are request in the gentoo bugzilla.

All bugs and feature request should be either send to justin at j-schmitz dot net or spamsuxx at gmail dot com.

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build 
sudo python setup.py install 
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

'''NOTE : '''If you experience problems with PyMOL OpenGL window (i.e. flickering) try disabling compiz.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

===xorg.conf for stereo in Fedora Core 6===
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:

<pre>
Driver "nvidia"
</pre>

Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.

<pre>
Section "Extensions"
Option "Composite" "Disable"
EndSection
</pre>

In Section "Screen" add the following line to enable quad-buffered stereo:

<pre>Option "Stereo" "3"</pre>

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

==Super-Large Files==
For loading files that require the majority of your system's memory, try tweaking your system's [http://certcities.com/editorial/columns/story.asp?EditorialsID=214 ulimit] before starting PyMOL. ''' ''Be warned, when your system uses its full amount of memory and swap space, it comes to a halt very quickly.'' '''
<source lang="bash">
# shows current setup
ulimit -a

# allows setting of a limit in current shell.
ulimit -v SizeInKB
</source>

Category:FAQ

2008-09-29T20:47:27Z

Warren: /* Others */

==Overview==
Please post your FAQs here. I suggest you write a Q&A style list with a short answer. More involved answers should link to its own page. Just my suggestion. Should we have topics? Please note, not all AQ are FAQ. Also, many answers to frequently recurring problems are probably best sought by searching for your terms in the Wiki.

===Installation===
Q: I've installed PyMol_0_98, and recently my structures have stopped displaying. I've tried uninstalling PyMol_0_98 and installing PyMol_0_97, and yet i've ran into the same problem...my .pdb files no longer display, although it is evident that they are being loaded and I can edit them.

Does anybody have any clue as to what might be the problem?
Thanks, shebsmehr

----
===Startup===
Q: I've installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even save the images I create in PyMol and obviously the mivie too.

Could you help me to solve these problems.
Thanks
Vittorio

A1: Vittorio, if I understand you correctly, then you need to (a) make sure you have the PDB file on your machine, say Desktop (or home directory, for *nix), then in the GUI click on, "File"->"Open" then use the dialog to find the file you want to load. You can save time if you know where the file is by just using PyMol's "load" command
load fileName, objectName
loads the fileName into a new object called objectName, for example,
load /tmp/1ggz.pdb, 1ggz

See [[Cmd load|load]],

A2: To save images you have a couple options. First, to save a quick raw screen dump type, "png fileName" to save a PNG image (IE and other programs can view these files). Or, secondly, if you prefer a higher quality image with ray-traced shadows and textures you can do, "ray" then, the above "png" command.

See [[Cmd ray|ray]], [[Cmd png|png]], [[:Category:Using_Pymol|Using PyMol]]

Hope this helps. If it didn't please restate your question to make it more clear.
----
Q: Hi I have a problem. For some reason PyMOl do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon. When I display the structure in "lines" or "sticks" everything is ok. Furthermore, other .pdb viewers dont have this problem. I have tried several things:
1. Upgraded to the newest version og PyMol.
2. Redefined secondary structure using the "alter command".
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.

None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)
Cheers
Kasper

----

Q: Can the startup settings be edited so that MacPyMol starts with a One-Button Mouse mode? Please advise.
A: echo "config_mouse one_button" >> ~/.pymolrc

----
Q: What I should write into the .pymolrc (Mandriva Linux) to be able open PyMol with .pdb or .pml from shell? I was able to run pymol *.pdb with old 0.99rc6 version, but then I upgraded Mandriva Linux and this option is not working anymore.

===Settings===
Q: I am wondering how to change the default settings for a color "spectrum". I would like to color by b-factor but not with the default spectrum but from white-to-red.

A: See [[Color#Color_by_Spectrum_Example]].
----
Q: I would like the distance labels generated with the 'distance' command to be single-digit only, e.g. 2.8 instead of 2.77. How can I do this? Thanks, MindFrog

A: Setting startup settings and python commands can be done in a file: ~/.pymolrc
E.g. command in there: cmd.set('label_distance_digits',1)
On my windows machine this is in C:\Documents and Settings\jurgen.WHELK.000\.pymolrc
===Commands===
Q: I want to move one object while keeping another fixed. How do I do this?

A: Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. (Warren DeLano answer)
----
Q: I'd like to select residues that are in contact with a surface, or else be able to select buried/non-buried residues, is there any way to do this ? [[User:Xevi|Xevi]] 03:52, 16 Jun 2006 (CDT)
----
Q: After using the usual mset command to rotate an object, states/frames are loaded into that object. However, using the "frame" command has odd behaviour (in comparison to loading a molecular dynamics trajectory into the state in which the "frame" command behaves normally). Can anyone explain this?

----

Q: How do I suppress the 'ExecutiveRMS' output while running cmd.pair_fit()?

----

Q: How does cmd.rms() choose a mapping between atoms in the selections? Exhaustive search over all possibilities?

----
Q: How do I select (especially, iterate through a set of) bonds? The existence of [http://www.pymolwiki.org/index.php/Cycle_Valence cycle valence] seems to imply that it can be done. Is this possible via the API?
----

===Export/Import===
Q: Is there any way to export PyMol models onto CAD standards (autocad, archicad) or 3D modeling software (blender, 3DStudio, Maya)? Thanks a lot.
----
Q: I am doing some MD simulations using CHARMM (not AMBER) and would like to visualize the .dcd files output by CHARMM. I understand that PyMol can open .trj files from AMBER but is there a way to open up these .dcd files and if not, are there any plans to implement this? Thank you for your time!

A: Answering my own question here. See: [[Load_Traj]]

===Others===
Q: I was wondering what the percentage given under the mutengensis wizard means? Thanks...
----
Q: Some of the bases in RNA helices are missing (not all in any given helix) when I am showing them in the CARTOON mode. How should I set it to get them shown? I tried the Secondary Structure Assignment commands, they did not work.
----
Q: Why does PyMol run version 2.3 of Python when I have Python 2.5 installed? How do I tell it to switch?
----
Q: How do I cite PyMOL?

A: DeLano, W.L. The PyMOL Molecular Graphics System. (2008) DeLano Scientific LLC, Palo Alto, CA, USA. http://www.pymol.org

Category:FAQ

2008-09-29T20:46:43Z

Warren: /* Others */

==Overview==
Please post your FAQs here. I suggest you write a Q&A style list with a short answer. More involved answers should link to its own page. Just my suggestion. Should we have topics? Please note, not all AQ are FAQ. Also, many answers to frequently recurring problems are probably best sought by searching for your terms in the Wiki.

===Installation===
Q: I've installed PyMol_0_98, and recently my structures have stopped displaying. I've tried uninstalling PyMol_0_98 and installing PyMol_0_97, and yet i've ran into the same problem...my .pdb files no longer display, although it is evident that they are being loaded and I can edit them.

Does anybody have any clue as to what might be the problem?
Thanks, shebsmehr

----
===Startup===
Q: I've installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even save the images I create in PyMol and obviously the mivie too.

Could you help me to solve these problems.
Thanks
Vittorio

A1: Vittorio, if I understand you correctly, then you need to (a) make sure you have the PDB file on your machine, say Desktop (or home directory, for *nix), then in the GUI click on, "File"->"Open" then use the dialog to find the file you want to load. You can save time if you know where the file is by just using PyMol's "load" command
load fileName, objectName
loads the fileName into a new object called objectName, for example,
load /tmp/1ggz.pdb, 1ggz

See [[Cmd load|load]],

A2: To save images you have a couple options. First, to save a quick raw screen dump type, "png fileName" to save a PNG image (IE and other programs can view these files). Or, secondly, if you prefer a higher quality image with ray-traced shadows and textures you can do, "ray" then, the above "png" command.

See [[Cmd ray|ray]], [[Cmd png|png]], [[:Category:Using_Pymol|Using PyMol]]

Hope this helps. If it didn't please restate your question to make it more clear.
----
Q: Hi I have a problem. For some reason PyMOl do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon. When I display the structure in "lines" or "sticks" everything is ok. Furthermore, other .pdb viewers dont have this problem. I have tried several things:
1. Upgraded to the newest version og PyMol.
2. Redefined secondary structure using the "alter command".
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.

None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)
Cheers
Kasper

----

Q: Can the startup settings be edited so that MacPyMol starts with a One-Button Mouse mode? Please advise.
A: echo "config_mouse one_button" >> ~/.pymolrc

----
Q: What I should write into the .pymolrc (Mandriva Linux) to be able open PyMol with .pdb or .pml from shell? I was able to run pymol *.pdb with old 0.99rc6 version, but then I upgraded Mandriva Linux and this option is not working anymore.

===Settings===
Q: I am wondering how to change the default settings for a color "spectrum". I would like to color by b-factor but not with the default spectrum but from white-to-red.

A: See [[Color#Color_by_Spectrum_Example]].
----
Q: I would like the distance labels generated with the 'distance' command to be single-digit only, e.g. 2.8 instead of 2.77. How can I do this? Thanks, MindFrog

A: Setting startup settings and python commands can be done in a file: ~/.pymolrc
E.g. command in there: cmd.set('label_distance_digits',1)
On my windows machine this is in C:\Documents and Settings\jurgen.WHELK.000\.pymolrc
===Commands===
Q: I want to move one object while keeping another fixed. How do I do this?

A: Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. (Warren DeLano answer)
----
Q: I'd like to select residues that are in contact with a surface, or else be able to select buried/non-buried residues, is there any way to do this ? [[User:Xevi|Xevi]] 03:52, 16 Jun 2006 (CDT)
----
Q: After using the usual mset command to rotate an object, states/frames are loaded into that object. However, using the "frame" command has odd behaviour (in comparison to loading a molecular dynamics trajectory into the state in which the "frame" command behaves normally). Can anyone explain this?

----

Q: How do I suppress the 'ExecutiveRMS' output while running cmd.pair_fit()?

----

Q: How does cmd.rms() choose a mapping between atoms in the selections? Exhaustive search over all possibilities?

----
Q: How do I select (especially, iterate through a set of) bonds? The existence of [http://www.pymolwiki.org/index.php/Cycle_Valence cycle valence] seems to imply that it can be done. Is this possible via the API?
----

===Export/Import===
Q: Is there any way to export PyMol models onto CAD standards (autocad, archicad) or 3D modeling software (blender, 3DStudio, Maya)? Thanks a lot.
----
Q: I am doing some MD simulations using CHARMM (not AMBER) and would like to visualize the .dcd files output by CHARMM. I understand that PyMol can open .trj files from AMBER but is there a way to open up these .dcd files and if not, are there any plans to implement this? Thank you for your time!

A: Answering my own question here. See: [[Load_Traj]]

===Others===
Q: I was wondering what the percentage given under the mutengensis wizard means? Thanks...
----
Q: Some of the bases in RNA helices are missing (not all in any given helix) when I am showing them in the CARTOON mode. How should I set it to get them shown? I tried the Secondary Structure Assignment commands, they did not work.
----
Q: Why does PyMol run version 2.3 of Python when I have Python 2.5 installed? How do I tell it to switch?
----
Q: How do I cite PyMOL?

DeLano, W.L. The PyMOL Molecular Graphics System (2008)
DeLano Scientific LLC, Palo Alto, CA, USA. http://www.pymol.org

Stereo 3D Display Options

2008-09-18T21:20:39Z

Warren: /* Who Says? */

Stereo 3D Display Options

2008-09-18T21:17:23Z

Warren: /* Active Stereo 3D (High Refresh) Projectors */

Stereo 3D Display Options

2008-09-18T21:16:11Z

Warren: /* DLP Projectors */

Stereo 3D Display Options

2008-09-18T16:54:42Z

Warren: /* LCD Displays */

Stereo 3D Display Options

2008-09-18T16:52:30Z

Warren: /* Passive Stereo 3D Adaptor Hardware for Active Stereo 3D Projectors */

Stereo 3D Display Options

2008-09-18T16:52:02Z

Warren: /* Who Say's? */

Stereo 3D Display Options

2008-09-18T16:51:18Z

Warren: /* DLP Projectors */

Stereo 3D Display Options

2008-09-18T16:46:08Z

Warren: /* Mirror-based Multi-LCD Solutions */