PyMOL Wiki - User contributions [en]

Get Names

2012-03-01T18:18:10Z

Harijay: Undo revision 10576 by Harijay (talk)

'''get_names_of_type''' returns a list of object and/or selection names.

===PYMOL API===
<source lang="python">
cmd.get_names_of_type( [string: "type"] )
</source>

===NOTES===
The object types are strings such as "object:molecule" for a molecule type and "object:map" for a map.

=== EXAMPLES ===
Truncate names of all molecules
<source lang="python">
# Get names for all molecules.
for x in cmd.get_names_of_type("object:molecule"): cmd.set_name(x,x[:5])
</source>

===SEE ALSO===
[[get_type]], [[count_atoms]], [[count_states]],[[get_names_of_type]]

[[Category:Commands|Get Names]]

Get Names

2012-03-01T18:16:26Z

Harijay:

Get Names

2012-03-01T18:14:45Z

Harijay: moved Get Names to Get Names of Type

Get Names

2012-03-01T18:12:14Z

Harijay:

Get Names

2012-03-01T18:11:35Z

Harijay:

'''get_names''' returns a list of object and/or selection names.

===PYMOL API===
<source lang="python">
cmd.get_names_of_type( [string: "type"] )
</source>

===NOTES===
The object types are strings such as "object:molecule" for a molecule type and "object:map" for a map.

=== EXAMPLES ===
Truncate names of all molecules
<source lang="python">
# Get names for all molecules.
for x in cmd.get_names_of_type("object:molecule"): cmd.set_name(x,x[:5])
</source>

===SEE ALSO===
[[get_type]], [[count_atoms]], [[count_states]],[[get_names_of_type]]

[[Category:Commands|Get Names]]

Get Names

2012-03-01T17:57:48Z

Harijay:

'''get_names''' returns a list of object and/or selection names.

===PYMOL API===
<source lang="python">
cmd.get_names( [string: "objects"|"selections"|"all"|"public_objects"|"public_selections"] )
</source>

===NOTES===
The default behavior is to return only object names.

=== EXAMPLES ===
Multiple alignments
<source lang="python">
# structure align all proteins in PyMOL to the protein named "PROT". Effectively a
# poor multiple method for multiple structure alignment.
for x in cmd.get_names("all"): cealign( "PROT", x)
</source>

===SEE ALSO===
[[get_type]], [[count_atoms]], [[count_states]],[[get_names_of_type]]

[[Category:Commands|Get Names]]

Internal gui

2012-02-13T18:11:08Z

Harijay: /* See Also */

= Overview =
The internal GUI is the openGL-based user interface (that is--not the TK-window). Here you can enable/disable proteins from view, color then, change their representation--a whole host of things. If you want a nice clean presentation mode, you can turn off the internal GUI using this setting.

<gallery>
Image:Ig_on.png|Internal GUI on
Image:Ig_off.png|Internal GUI off
</gallery>

= Syntax =
<source lang="python">
# turn the internal gui off
set internal_gui, off

# turn it back on
set internal_gui, on
</source>

= See Also =
[[:Category:GUI|GUI Category]] , [[Group]]

[[Category:GUI|GUI Category]]
[[Category:Settings]]

Group

2012-02-11T16:51:36Z

Harijay:

The [[Group]] command creates or updates a "group" object. The grouped objects are collected underneath a '''+''' sign in the object tree (see images) in the Pymol Internal Gui.

[[Group]] is tremendously helpful with multi-state or multi-structure sessions. Wildcards work great, for example:
<source lang="python">
# put all of objState into the group "ensemble".
group ensemble, objState*
</source>

<gallery>
Image:group_off.png|Three EF-Hand proteins loaded into PyMOL
Image:group_on1.png|Applied the group command to the proteins via: "group efHand, *"
Image:group_on2.png|The plus was clicked and expanded to show the hierarchy of objects.
</gallery>

== Usage ==
<source lang="python">
group name, members, action
</source>

== Examples ==

=== Creating, opening and closing ===
<source lang="python">
group efHand, 1cll 1ggz 1sra

# allow addition and removal from the group
group efHand, open
# disallow addition/removal from the group
group efHand, close
</source>

=== More advanced usage of groups and naming ===

<source lang="python">
# names with dots are treated special

set group_auto_mode, 2

# load the example protein

load $TUT/1hpv.pdb, 1hpv.other

# create the new entry called ".protein" in group 1hpv

extract 1hpv.protein, 1hpv.other and polymer

# create ".ligand in the 1hpv group

extract 1hpv.ligand, 1hpv.other and organic

# supports wildcards

show sticks, *.ligand

hide lines, *.protein

show surface, *.protein within 6 of *.ligand

show lines, byres *.protein within 4 of *.ligand

set two_sided_lighting

set transparency, 0.5

set surface_color, white

# Also, to lexicographically sort the names in the control panel:

order *, yes
</source>
== Notes ==
Group objects can usually be used as arguments to commands. It can be processed as a group or as a selection, in which case all the atoms from all objects in the group will be used.

== See Also ==
[[ungroup]] [[order]] [[select]]

[[Category:Commands|Group]]

MovieSchool 5

2011-10-15T11:35:41Z

Harijay: /* Representations */

== Putting It All Together ==
Now that we understand the basic PyMOL commands for movie making, we build a few ideas--which have already been hinted at--that lead to the final goal: allowing you to generate PyMOL movies to tell the stories you want to tell. We start simple and build up the complexity. Here's an outline of the ideas:
* '''camera motions'''—just moving the camera around your scene
* '''object motions'''—keeping the camera still, but moving the objects around the scene
* '''camera & object motions '''—moving both the camera and objects around
* '''representations'''—changing representations in a movie (eg. sticks to cartoons to surface; hiding/showing, etc.)
* '''motions & representations '''—adding all the motions and representations together
* '''extras'''—pseudoatom labels; scene messages, etc.
* '''final example movies'''—some examples combining the above knowledge

If you've read through most the above article on movie making, then these sections should be more of a review. There are some tricks in here that might be worth reading, however.

Many of the movie scripts below assume that you have readied PyMOL for movie generation. To do that use the following code:
<source lang="python">
reinitialize
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
config_mouse three_button_motions, 1

# initialize a 100 frame movie
mset 1 x100
</source>

===Camera Motions===
One of our first movies above was a very simple zoom on an atom in an amino acid. The first 'scene' was the entire amino acid and the 2nd 'scene' was the zoomed in atom. We just connected the two scenes and asked PyMOL to make the transition between the two smooth. This is the idea of camera motions in PyMOL. (You may not know that when you click on a protein and rotate it or drag it in PyMOL you're actually moving the camera, not the protein.)

Assuming you had readied PyMOL to make your movie to get a camera motion you do the following:
* '''save the camera's first position information''': Once you have the protein/object aligned and shown in the representation of your choice, set the '''camera''' position information
<source lang="python">
# goto the first frame
frame 1
# store the CAMERA positions ONLY
mview store
</source>
* '''save the cameras second position information''': Now using the mouse (or scripted commands) move the camera to its new position--say zooming in on an important ligand or catalytic residue. Once that's done, tell PyMOL to store the new camera position in this frame:
<source lang="python">
# goto the first frame
frame 88
# store the CAMERA positions ONLY
mview store

# now link the two stored camera positions together:
mview reinterpolate

# play your movie
mplay
</source>

Hints:
* '''mview reinterpolate, power=1" will turn off the smoothed starting and stopping of camera motions between the scenes. The smoothing gives a nicer feel to transitions. Try both, see which you prefer.
* check out mview's other options--like 'wrap'
* using the three_button_motions option, you can pretty much make the entire movie w/your mouse: All->M->Store is the same as, ''mview store'', and All->M->Reinterpolate is the same as ''mview reinterpolate''.
* '''[[mview]] reset''' unstores the camera position information for this frame.

==== Camera Motions Movie Example ====
This idea should be pretty sound at this point, but examples rock, so here's another. The pattern is:
* frame XYZ
* script the view
* mview store

<source lang="python">
# setup PyMOL for movies
reinitialize
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
config_mouse three_button_motions, 1

fetch 1te1, async=0
extract AA, c. A
extract BB, c. B
color marine, AA
color grey, BB
as surface, BB
as cartoon, AA

mset 1 x620

orient

wizard message, "Can you see the blue protein inhibiting the gray protein?"

frame 1
mview store
frame 30
mview store

### cut below here and paste into script ###
set_view (\
0.307660401, 0.011366921, 0.951428533,\
0.930296898, -0.213488042, -0.298277378,\
0.199727684, 0.976880252, -0.076255992,\
0.000000000, 0.000000000, -196.781448364,\
27.129878998, 68.309677124, 51.827075958,\
155.143981934, 238.418914795, -20.000000000 )
### cut above here and paste into script ###

# slowly show the inhibition
frame 120
mview store

# wait 3 seconds
frame 180
mview store

# define the inhib as the binding loop
select inhib, AA and i. 148-155
select (none)

# slowly zoom in
frame 300
zoom inhib
mview store

# stop a second
frame 330
mview store

# look around the binding pocket
frame 390
turn y, 150
mview store

# wrap back more quickly...
frame 420
turn y, -150
mview store

# one more gratuitous view
frame 500
### cut below here and paste into script ###
set_view (\
0.943371952, 0.309539229, -0.119302809,\
-0.044248745, -0.239008784, -0.970008850,\
-0.328769624, 0.920357347, -0.211777285,\
0.000000000, 0.000000000, -30.773454666,\
35.418403625, 72.805625916, 52.437019348,\
20.233829498, 41.313076019, -20.000000000 )
### cut above here and paste into script ###
mview store

frame 560
mview store

mview reinterpolate
mplay
</source>

===Object Motions===

Now that we're experts at moving the PyMOL camera around, let's start moving objects around while keeping the camera steady. To do this '''you must have matrix_mode set to 1''', otherwise PyMOL won't save your object's repositioning.

Let's use the same proteins as from the above inhibitor example. This time, let's try to get a simple movie that shows one of the proteins and then have the other one fly in to do the inhibiting.

<source lang="python">
# setup PyMOL for movies
reinitialize
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
config_mouse three_button_motions, 1

# download the complex and setup it up
fetch 1te1, async=0
extract AA, c. A
extract BB, c. B
color marine, AA
color grey, BB
as surface, BB
as cartoon, AA

# intialize the movie
mset 1 x410

# orient the scene
set_view (\
0.423117876, 0.061672822, 0.903973043,\
0.789699256, -0.514252067, -0.334546506,\
0.444237947, 0.855418444, -0.266292989,\
0.000107866, -0.000027858, -196.784057617,\
28.171787262, 70.919288635, 52.095287323,\
155.143981934, 238.418914795, -20.000000000 )

# move the inhibitor off the screeen
translate [0,0,100], object=AA

# first movie scene
frame 1
wizard message, "Let's watch the binder float it, while the camera doesn't move."
mview store, object=AA
mview store, object=BB

# 2 second pause for the user to catch up
frame 60
mview store, object=AA
mview store, object=BB

frame 300
# slide the inhibitor in from over the camera. :-)
translate [0,0,-100], object=AA
mview store, object=AA
mview interpolate, object=AA

# store & wait 2 seconds...
frame 360
mview store, object=AA
mview store, object=BB
mview reinterpolate, object=AA
mview reinterpolate, object=BB

# 'explode' apart
frame 380
translate [-70, 70, 70], object=AA
translate [70, -70, -70], object=BB
mview store, object=AA
mview store, object=BB
mview reinterpolate, object=AA
mview reinterpolate, object=BB

mplay
</source>

Hints:
* Use the mouse to get the 'right orientation & zoom'. Then use [[get_view]] to get the view matrix. Finally, store that camera-position view matrix in your script. Works every time.
* For object motions, the command '''translate [-70,70,70], object=AA''' would be the same as using the mouse and moving the object AA -70 units on the X-axis, +70 units on the Y and 70 on the Z. If you don't use the '''object=''' you will not get the desired effect.
* For the above 'explosion' you can get quick motions by interpolating a large change over just a few frames.

===Camera & Object Motions===
Now let's combine the above two sections into one movie that has both object and camera motions. This should be cool...

<source lang="python">
# setup PyMOL for movies
reinitialize
set movie_auto_interpolate, off
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
config_mouse three_button_motions, 1

# download the complex and set it up
fetch 1te1, async=0
extract AA, c. A
extract BB, c. B
color marine, AA
color grey, BB
as surface, BB
as cartoon, AA

mset 1 x120
# overview of the scene
frame 1
mview store
mview store, object=AA
mview store, object=BB

# zoom into the binding pocket- setting the view means
# that this will be a camera motion from frames 1 to 120.
frame 120
set_view (\
0.993863702, 0.110482253, -0.005255031,\
0.054543663, -0.530888498, -0.845684826,\
-0.096224494, 0.840209842, -0.533656776,\
0.000000000, 0.000000000, -50.366786957,\
34.781314850, 71.208221436, 52.535022736,\
39.709556580, 61.024017334, -20.000000000 )
mview store
mview store, object=AA
mview store, object=BB

# wiggle the inhibitor, like it's trying to escape
python
for x in range(20):
cmd.madd("1 x3"); cmd.frame(1000);
cmd.rotate("x", 2.0, object="AA")
cmd.mview("store", object="AA")
cmd.mview("store")
cmd.mview("interpolate", object="AA")
cmd.mview("reinterpolate")

cmd.madd("1 x3"); cmd.frame(1000);
cmd.rotate("x", -2.0, object="AA")
cmd.mview("store", object="AA")
cmd.mview("store")
cmd.mview("interpolate", object="AA")
cmd.mview("reinterpolate")
python end

mview store

madd 1 x60
frame 240
mview store
mview store, object=AA
mview store, object=BB

mview interpolate, object=AA
mview interpolate, object=BB
mview reinterpolate

mplay

</source>

===Representations===

Scenes are the only way to change representations (eg sticks to cartoon). In PyMOL to show representation changes we need to have a list of scenes, that we then assign to a given frame. Once this is done we can reinterpolate through scenes to have beautifully smooth transitions.

PyMOL makes it very easy to setup your scenes--for that ''look''--and save them in a stack (and, now, even move them around). We covered scenes already in the tutorial, so please check that if you need more help on scenes, or see [[:Category:Scenes]] for more commands and hints.

In PyMOL, to attach a scene to a frame (or, technically a frame to a scene) we simply do the following:
<source lang="python">
mview store, scene=sceneName
</source>

Let's take a look at a simple movie that changes the representation of some object. This will show a tryptophan going from lines to sticks and back.
<source lang="python" line=1>
set scene_buttons, 1
set movie_panel, 1

# make a 90 frame movie, all STATE 1.
mset 1 x90

# load a trypotphan fragment
frag trp

# Tell PyMOL to call this current view '001'.
scene 001, store
# goto frame 1 and store this scene & camera
frame 1
mview store, scene=001

# setup the next 'view'
as sticks
scene 002, store

# goto frame 60 and show sticks
frame 45
mview store, scene=002

mview reinterpolate
mplay
</source>

To show you how easy adding camera motions + representations is, simply insert after line 17 (''as sticks'') a new line 18 that only has
<source lang="python">
orient
</source>

Here's what's happening in the movie, above. Lines 1—2 set PyMOL up to show you [[scene_buttons|scene buttons]] and the [[Movie_panel|movie panel]]. Line 5 makes a 90 '''frame''' movie that only spans the first state. Line 8 makes the TRP fragment from PyMOL's stored knowledge of residues. Line 11 asks PyMOL to store this current 'view' as a [[scene]] and call that scene ''001''. Now that a scene is made, we need to associate with a frame. So, we goto frame 1 in line 13. In line 14 we actually make the scene-to-frame assignment with the [[mview]] store command, specifying the mapping between scene 001 and frame 1. Lines 17 and 18 change the representation from lines to sticks and then orients the TRP residue (which causes the camera to move). In line 19, we save this new camera position and the sticks representation of TRP in the scene called ''002''. Next, in line 22, we go somewhere ahead in the movie, here 1/2 way to the end. Line 23 assigns scene ''002'' to frame 45. Lastly, because we changed the camera position, we need to reniterpolate it's movement, and that's done in line 24. As you know [[mplay]] just plays the movie.

* '''Hint''': Clear frames with '''mview clear'''
* '''Hint''': Clear scenes with '''scene sceneName, delete'''; you can delete all scenes with '''scene *, delete'''.

Now that we have that, let's learn more complex tricks with motion and representations!

===Motions & Representations ===

Let's look at the inhibitor complex again, (pdb 1TE1). This time, we would like to make a more compex movie that shows moving objects (not the camera) and changing representations. I do not want wrapping b/c I slide the molecule off the sceen. To ensure that, I allow 0 transition frames, by setting the last frame in the movie by '''mview store'''.

<source lang="python">
# b/c there will be motions, we need matrix_mode
reinitialize
set matrix_mode, 1
set scene_buttons, 1
set movie_panel, 1

# setup the movie for 410 frames
mset 1 x240

# load the complex & set it up
fetch 1te1, async=0
as cartoon
remove resn HOH
extract AA, c. A
extract BB, c. B

# zoom in on the binding pocket
### cut below here and paste into script ###
set_view (\
0.478582859, -0.269358903, 0.835705996,\
0.805654645, -0.243718535, -0.539927721,\
0.349110991, 0.931690335, 0.100370787,\
0.000000000, 0.000000000, -49.810981750,\
35.418403625, 72.805625916, 52.437019348,\
39.271358490, 60.350605011, -20.000000000 )
### cut above here and paste into script ###

# store object AA's position
frame 1
scene 001, store, message="This doesn't quite give us a good feel for what's going on."
mview store, object=AA
mview store, scene=001

# change up the scene a bit
frame 60
color grey, AA
color marine, BB
scene 002, store, message="Recoloring helps a little."
mview store, scene=002

# show chain B as surface
frame 120
as surface, BB
mview store, object=AA
scene 003, store, message="Surface helps alot."
mview store, 120, scene=003

# show more
frame 180
select inhib, AA and i. 148-155;
show sticks, inhib
color magenta, inhib
select nn, BB within 7 of inhib; deselect;
set transparency, 0.65, nn
show sticks, nn
set_bond stick_color, chartreuse, nn
scene 004, store, message="Coloring, transparency, and other objects help more..."
mview store, object=AA
mview store, 180

# move AA away
frame 240
translate [20, 10, 80], object=AA
mview store, object=AA
mview reinterpolate, object=AA
mview store, 240
mview reinterpolate

</source>

* '''Hint''': Use '''mview store, frameNo, scene=sceneName''' to save complex scenes. If you do:
<source lang="python">
frame X
scene Y
mview store X, scene=Y
</source>
then the PyMOL GUI may not have caught up to the correct place before saving the scene information.
* '''Hint''': Things can get confusing with frames, states and whatnot. A good idea is to ALWAYS set your frame when setting a new scene. If you don't '''mview store''' might save a different frame number than you think you're on. Or, you can save the frame number too with, '''mview store, frameNo, scene=XXX, object=YYY'''.
* '''Hint''': Use [[deselect]] in a script to hide the dots from making a new selection.
* '''Hint''': Use [[set_bond]] to set bond properties, like colors, on [[sticks]] representations.

=== Extras ===

[[MovieSchool_4| ← Previous Lesson]] [[MovieSchool_6| Next Lesson →]]

[[Category:Movies]]
[[Category:Tutorials]]

Stereo 3D Display Options

2010-02-01T15:47:05Z

Harijay: /* 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 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. Quad buffered stereo works with a [http://en.wikipedia.org/wiki/Nvidia_Quadro G8x based graphics core] or better Quadro FX card with the 3 pin mini din stereo connector (e.g. Quadro FX 3700), 195.22 nvidia linux binary driver, and the nvidia 3d vision kit. [http://en.wikipedia.org/wiki/Nvidia_Quadro Quadro-FX Cards with the NV41/42/45GL core] do not support stereo with the nvidia 3D vision kit even if they have a 3-pin mini din connector in the back. USB only based stereo with the 3D vision kit works only in MS Windows (e.g. with a low end Quadro FX 370 that has no 3 pin mini din stereo connector). For more information see this forum post [http://forums.nvidia.com/index.php?showtopic=91072&view=findpost&p=968627 at the Nvidia Forums] - SP
:: '''WARNING:''' NVidia 3D NVision kit only supports directX software for GeForce (gaming cards) on Windows; users are reporting that they are not able to run PyMOL with NVision with these cards. Get a newer model low end quadro (> G8x graphics core) without the 3 pin mini din (e.g. Quadro 370) or with the 3 pin mini din (e.g. Quadro 3700) for Windows.

==== NVision Setup ====
These instructions might work for XP/Vista.

Setup:

- A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm
- A recent Quadro series graphics card such as an FX 380 or 570.
- A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses).
- Windows XP 32 bit

You need the 190+-series graphics driver for Windows XP:

http://www.nvidia.com/object/winxp_190.38_beta.html

and the 190-series 3D Vision driver for Windows Vista:

http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_190.38.html

Instructions:

* Uninstall the existing display drivers, disconnect the USB emitter, and reboot.
* Run the Window XP graphics driver installer and reboot.
* Launch the Vista 3D Vision driver in order to extract the files you need, but do not yet click Next on the Welcome page...just leave it open for now...do not close the installer.
* Plug in the USB emitter. Windows should throw up the Found New Hardware Wizard**. Choose "No, not this time" and go to the Next page. Select "install from a list or specific location" and click Next to continue. Choose "Search for the best driver", "include this specific location...", and click Browse. Now c comes the hard part: you must select the folder which contains the file "nvstusb.inf". On my system, that file was unpacked into c:\Documents and Settings\Warren~1~000\Locals~1\Temp\pft16~tmp - your copy may be in a similar location. You may need to use Windows Search to find the file. Once you've chosen the correct folder, click Ok and then Next. You may then be asked to locate "nvstusb.sys", which should be in the same folder. Click Ok once you've found the file, and then Finish. This should complete installation of the USB driver.
**If Windows doesn't throw up the Found New Hardware Wizard, use the
Device Manager to locate the device and then update the driver for the
device using the same process described above.
* Now allow the 3D Vision Installer to continue. Since your on XP, not Vista, it will complain and throw up one warning and one error message, but it should still complete. Reboot when prompted. The rest of the instructions are basically the same as for Vista:
* Open the NVIDIA Control Panel, and increase the display refresh rate to 120 Hz using the display resolution tab. Then go to the 3D Settings tab and set the Stereo display mode to "Generic active stereo (with NVIDIA IR Emitter)", click Apply, and then set Stereo - enable mode to "on", click Apply, and then close the NVIDIA control panel.
* Launch PyMOL 1.2r1 for Windows. You should get the message: "OpenGL quad-buffer stereo 3D detected and enabled."
* Now load a PDB file and issue "stereo on". The emitter should light up and the glasses should activate.

Congratulations -- you should now be able to view PyMOL molecular structures in stereo 3D on a 120 Hz LCD using Windows XP!

=== 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
* SP = Sabuj Pattanayek of the Center For Structural Biology, Vanderbilt University

[[Category:Hardware_Options]]
[[Category:Stereo_3D_Display]]
[[Category:Stereo]]

Covers

2009-11-18T23:44:26Z

Harijay:

= PyMOL-created Journal Covers =
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.

Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.

<gallery perrow="5">
Image:Cover_royal_soc_small.png |[http://pymolwiki.org/index.php/File:Cover_royal_soc_small.png Philosophical Transactions of The Royal Society, B : Biological Sciences Jan, 2009 ]
Image:Image_large.png |[http://pymolwiki.org/index.php/File:Image_large.png MD simulation of protein-protein binding ]'''Pymol generated Movie is avialable inside pdf'''[[http://www.pymolwiki.org/index.php/File:SH3.pdf]] ''' or high quality AVI format'''[http://gepard.bioinformatik.uni-saarland.de/old_html/material/dl/SH3_large.avi]
Image:Cover_JCIM_2008_48-10.png|[http://pubs.acs.org/action/showLargeCover?issue=329743592 J. Chem. Inf. Model., 2008, 48 (10)]
Image:Science090410.jpg|[http://www.sciencemag.org/content/vol324/issue5924/index.dtl Protein Dynamics]
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.
Image:071213nature.pdf.jpg|'''Pumping Ions''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007.
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.

Image:050923_h.a.steinberg_JBC.jpg|'''GalNAc kinase''', [http://www.jbc.org/content/vol280/issue38/cover.shtml JBC], September 23, 2005 Cover, Volume 280, Issue 38.
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.
Image:050624_h.a.steinberg_jmb1.jpg|[http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996509994%23597371%23FLA%23&_cdi=6899&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bc37bcef231976694d0fbe8920ef596 JMB], June 24, 2005 Cover, Volume 349, Issue 5.
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.
Image:apr2003_ProtSci.png|''Pae'' SmAP1 14-mers, [http://www3.interscience.wiley.com/journal/121602086/issue ''Protein Science'', April 2003].
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]
Image:CRP_nature_cover1.jpg|''Nature'', April 27th, 2006.
</gallery>

File:Cover royal soc small.png

2009-11-18T23:42:07Z

Harijay: Cover Illustration made in Pymol of E.coli CLC_ec1 chloride proton antiporter with ion conduits generated in program Mole and visualized as pymol cgo spheres. Illustration appeared on the Jan 2009 Issue of the Philosophical Transactions of The Royal Socie

Cover Illustration made in Pymol of E.coli CLC_ec1 chloride proton antiporter with ion conduits generated in program Mole and visualized as pymol cgo spheres. Illustration appeared on the Jan 2009 Issue of the Philosophical Transactions of The Royal Society : Section B Biological Sciences detailing "Discussion Meeting Issue ‘Membrane transport in flux: the ambiguous interface between channels and pumps’ organized by F. M. Ashcroft, D. Gadsby and C. Miller "

Covers

2009-11-18T15:39:02Z

Harijay: Undo revision 7626 by Harijay (Talk)

= PyMOL-created Journal Covers =
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.

Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.

<gallery perrow="5">
Image:1514.cover.gif |[http://pymolwiki.org/index.php/File:1514.cover.gif Philosophical Transactions of The Royal Society, B : Biological Sciences Jan, 2009 ]
Image:Image_large.png |[http://pymolwiki.org/index.php/File:Image_large.png MD simulation of protein-protein binding ]'''Pymol generated Movie is avialable inside pdf'''[[http://www.pymolwiki.org/index.php/File:SH3.pdf]] ''' or high quality AVI format'''[http://gepard.bioinformatik.uni-saarland.de/old_html/material/dl/SH3_large.avi]
Image:Cover_JCIM_2008_48-10.png|[http://pubs.acs.org/action/showLargeCover?issue=329743592 J. Chem. Inf. Model., 2008, 48 (10)]
Image:Science090410.jpg|[http://www.sciencemag.org/content/vol324/issue5924/index.dtl Protein Dynamics]
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.
Image:071213nature.pdf.jpg|'''Pumping Ions''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007.
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.

Image:050923_h.a.steinberg_JBC.jpg|'''GalNAc kinase''', [http://www.jbc.org/content/vol280/issue38/cover.shtml JBC], September 23, 2005 Cover, Volume 280, Issue 38.
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.
Image:050624_h.a.steinberg_jmb1.jpg|[http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996509994%23597371%23FLA%23&_cdi=6899&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bc37bcef231976694d0fbe8920ef596 JMB], June 24, 2005 Cover, Volume 349, Issue 5.
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.
Image:apr2003_ProtSci.png|''Pae'' SmAP1 14-mers, [http://www3.interscience.wiley.com/journal/121602086/issue ''Protein Science'', April 2003].
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]
Image:CRP_nature_cover1.jpg|''Nature'', April 27th, 2006.
</gallery>

Covers

2009-11-18T15:36:57Z

Harijay: /* PyMOL-created Journal Covers */

= PyMOL-created Journal Covers =
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.

Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.

<gallery perrow="5">
Image:Image_large.png |[http://pymolwiki.org/index.php/File:Image_large.png MD simulation of protein-protein binding ]'''Pymol generated Movie is avialable inside pdf'''[[http://www.pymolwiki.org/index.php/File:SH3.pdf]] ''' or high quality AVI format'''[http://gepard.bioinformatik.uni-saarland.de/old_html/material/dl/SH3_large.avi]
Image:Cover_JCIM_2008_48-10.png|[http://pubs.acs.org/action/showLargeCover?issue=329743592 J. Chem. Inf. Model., 2008, 48 (10)]
Image:Science090410.jpg|[http://www.sciencemag.org/content/vol324/issue5924/index.dtl Protein Dynamics]
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.
Image:071213nature.pdf.jpg|'''Pumping Ions''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007.
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.

Image:050923_h.a.steinberg_JBC.jpg|'''GalNAc kinase''', [http://www.jbc.org/content/vol280/issue38/cover.shtml JBC], September 23, 2005 Cover, Volume 280, Issue 38.
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.
Image:050624_h.a.steinberg_jmb1.jpg|[http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996509994%23597371%23FLA%23&_cdi=6899&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bc37bcef231976694d0fbe8920ef596 JMB], June 24, 2005 Cover, Volume 349, Issue 5.
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.
Image:apr2003_ProtSci.png|''Pae'' SmAP1 14-mers, [http://www3.interscience.wiley.com/journal/121602086/issue ''Protein Science'', April 2003].
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]
Image:CRP_nature_cover1.jpg|''Nature'', April 27th, 2006.
</gallery>

Covers

2009-11-18T15:29:07Z

Harijay:

= PyMOL-created Journal Covers =
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.

Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.

<gallery perrow="5">
Image:1514.cover.gif |[http://pymolwiki.org/index.php/File:1514.cover.gif Philosophical Transactions of The Royal Society, B : Biological Sciences Jan, 2009 ]
Image:Image_large.png |[http://pymolwiki.org/index.php/File:Image_large.png MD simulation of protein-protein binding ]'''Pymol generated Movie is avialable inside pdf'''[[http://www.pymolwiki.org/index.php/File:SH3.pdf]] ''' or high quality AVI format'''[http://gepard.bioinformatik.uni-saarland.de/old_html/material/dl/SH3_large.avi]
Image:Cover_JCIM_2008_48-10.png|[http://pubs.acs.org/action/showLargeCover?issue=329743592 J. Chem. Inf. Model., 2008, 48 (10)]
Image:Science090410.jpg|[http://www.sciencemag.org/content/vol324/issue5924/index.dtl Protein Dynamics]
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.
Image:071213nature.pdf.jpg|'''Pumping Ions''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007.
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.

Image:050923_h.a.steinberg_JBC.jpg|'''GalNAc kinase''', [http://www.jbc.org/content/vol280/issue38/cover.shtml JBC], September 23, 2005 Cover, Volume 280, Issue 38.
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.
Image:050624_h.a.steinberg_jmb1.jpg|[http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996509994%23597371%23FLA%23&_cdi=6899&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bc37bcef231976694d0fbe8920ef596 JMB], June 24, 2005 Cover, Volume 349, Issue 5.
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.
Image:apr2003_ProtSci.png|''Pae'' SmAP1 14-mers, [http://www3.interscience.wiley.com/journal/121602086/issue ''Protein Science'', April 2003].
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]
Image:CRP_nature_cover1.jpg|''Nature'', April 27th, 2006.
Image:1514.cover.gif| ''Philosophical Transactions of The Royal Society: Section B Biological Sciences'', 2009, ‘Membrane transport in flux: the ambiguous interface between channels and pumps’
</gallery>

File:1514.cover.gif

2009-11-18T15:09:37Z

Scene

2009-06-03T16:00:43Z

Harijay: /* SEE ALSO */

===DESCRIPTION===
'''scene''' makes it possible to save and restore multiple scenes scene within a single session. A scene consists of the view, all object activity information, all atom-wise visibility, color, representations, and the global frame index.

===USAGE (newer v1.1.b4)===
<source lang="python">
scene [key [,action [, message, [ new_key=new-key-value ]]]]
</source>

Arguments:
*key = string, new, auto, or *: use new for an automatically numbered new scene, use auto for the current scene (if one exists), and use * for all scenes (clear and recall actions only).
*action = store, recall, insert_after, insert_before, next, previous, update, rename, clear or append: (default = recall). If rename, then a new_key argument must be explicitly defined.
* message = string: a text message to display with the scene.
* new_key = string: the new name for the scene

===USAGE (older)===
<source lang="python">
scene key [,action [,message [ ,view [,color [,active [,rep [,frame]]]]]]]
scene *
</source>

Arguments:
*key can be any string
*action should be 'store' or 'recall' (default: 'recall')
*view: 1 or 0 controls whether the view is stored
*color: 1 or 0 controls whether colors are stored
*active: 1 or 0 controls whether activity is stored
*rep: 1 or 0 controls whether the representations are stored
*frame: 1 or 0 controls whether the frame is stored

===PYMOL API===
<source lang="python">
cmd.scene(string key,string action,string-or-list message,int view,
int color, int active, int rep, int frame)
</source>

===EXAMPLES===
Simple Examples.
<source lang="python">
scene F1, store
scene F2, store, This view shows you the critical hydrogen bond.

scene F1
scene F2
</source>

This example shows how to use scenes in a movie!
<source lang="python">
# SUMMARY
#

# This script demonstrates one way of creating a movie from scenes.
# It assumes that we have three scenes, each running for 10 seconds
# (300 frames apiece) including 2-second transitions.

# 1) Load or create content for three scenes (this could just as easily
# come from a session file).

load $TUT/1hpv.pdb
util.cbc
turn x,180
orient
as cartoon
scene 001, store

show sticks, organic
orient organic
scene 002, store

hide cartoon
show lines, byres organic expand 5
turn x,45
turn y,45
scene 003, store

# 2) Specify a 30-second movie -- state 1, 900 frames at 30 frames per second.

mset 1 x900

# 3) Program scene matrices as movie views at appopriate frames
# and also add y-axis rocking between scenes.

scene 001, animate=0
mview store, 1
mview store, 240

turn y,-30
mview store, 70
turn y,60
mview store, 170

scene 002, animate=0
mview store, 300
mview store, 540

turn y,-30
mview store, 370
turn y,60
mview store, 470

scene 003, animate=0
mview store, 600
mview store, 840

turn y,-30
mview store, 670
turn y,60
mview store, 770

# 4) Now interpolate the movie camera.

mview interpolate
mview smooth
mview smooth

# 5) Activate scene content at the appropriate movie frames.

mdo 1: scene 001, view=0, quiet=1
mdo 240: scene 002, view=0, quiet=1
mdo 540: scene 003, view=0, quiet=1
mdo 840: scene 001, view=0, quiet=1

# 6) Force frame 1 content to load.

rewind

# 6) And play the movie.

mplay
</source>

*Courtesy of Warren DeLano.

===NOTES===
* To scroll through your frames, as in a presentation, just use the PG-UP and PG-DN keys. Very handy.
*Scenes F1 through F12 are automatically bound to function keys provided that "set_key" hasn't been used to redefine the behaviour of the respective key.
*If you have a script that modifies the representation of the molecules and stores them, quickly, then the stored frames may not be up to date. I suggest calling "refresh" between the commands.

===SEE ALSO===
[[Cmd view]], [[Cmd set_view]], [[Cmd get_view]], [[Movie_from_scenes]]

===DEVELOPMENT TO DO===
Add support for save/restore of a certain global and object-and-state specific settings, such as: state, surface_color, ribbon_color, stick_color, transparency, sphere_transparency, etc. This would probably best be done by defining a class of "scene" settings which are treated in this manner. The current workaround is to create separate objects which are enabled/disabled differentially.

[[Category:Commands|scene]]
[[Category:States]]

Scene

2009-06-03T16:00:32Z

Harijay: /* SEE ALSO */

===DESCRIPTION===
'''scene''' makes it possible to save and restore multiple scenes scene within a single session. A scene consists of the view, all object activity information, all atom-wise visibility, color, representations, and the global frame index.

===USAGE (newer v1.1.b4)===
<source lang="python">
scene [key [,action [, message, [ new_key=new-key-value ]]]]
</source>

Arguments:
*key = string, new, auto, or *: use new for an automatically numbered new scene, use auto for the current scene (if one exists), and use * for all scenes (clear and recall actions only).
*action = store, recall, insert_after, insert_before, next, previous, update, rename, clear or append: (default = recall). If rename, then a new_key argument must be explicitly defined.
* message = string: a text message to display with the scene.
* new_key = string: the new name for the scene

===USAGE (older)===
<source lang="python">
scene key [,action [,message [ ,view [,color [,active [,rep [,frame]]]]]]]
scene *
</source>

Arguments:
*key can be any string
*action should be 'store' or 'recall' (default: 'recall')
*view: 1 or 0 controls whether the view is stored
*color: 1 or 0 controls whether colors are stored
*active: 1 or 0 controls whether activity is stored
*rep: 1 or 0 controls whether the representations are stored
*frame: 1 or 0 controls whether the frame is stored

===PYMOL API===
<source lang="python">
cmd.scene(string key,string action,string-or-list message,int view,
int color, int active, int rep, int frame)
</source>

===EXAMPLES===
Simple Examples.
<source lang="python">
scene F1, store
scene F2, store, This view shows you the critical hydrogen bond.

scene F1
scene F2
</source>

This example shows how to use scenes in a movie!
<source lang="python">
# SUMMARY
#

# This script demonstrates one way of creating a movie from scenes.
# It assumes that we have three scenes, each running for 10 seconds
# (300 frames apiece) including 2-second transitions.

# 1) Load or create content for three scenes (this could just as easily
# come from a session file).

load $TUT/1hpv.pdb
util.cbc
turn x,180
orient
as cartoon
scene 001, store

show sticks, organic
orient organic
scene 002, store

hide cartoon
show lines, byres organic expand 5
turn x,45
turn y,45
scene 003, store

# 2) Specify a 30-second movie -- state 1, 900 frames at 30 frames per second.

mset 1 x900

# 3) Program scene matrices as movie views at appopriate frames
# and also add y-axis rocking between scenes.

scene 001, animate=0
mview store, 1
mview store, 240

turn y,-30
mview store, 70
turn y,60
mview store, 170

scene 002, animate=0
mview store, 300
mview store, 540

turn y,-30
mview store, 370
turn y,60
mview store, 470

scene 003, animate=0
mview store, 600
mview store, 840

turn y,-30
mview store, 670
turn y,60
mview store, 770

# 4) Now interpolate the movie camera.

mview interpolate
mview smooth
mview smooth

# 5) Activate scene content at the appropriate movie frames.

mdo 1: scene 001, view=0, quiet=1
mdo 240: scene 002, view=0, quiet=1
mdo 540: scene 003, view=0, quiet=1
mdo 840: scene 001, view=0, quiet=1

# 6) Force frame 1 content to load.

rewind

# 6) And play the movie.

mplay
</source>

*Courtesy of Warren DeLano.

===NOTES===
* To scroll through your frames, as in a presentation, just use the PG-UP and PG-DN keys. Very handy.
*Scenes F1 through F12 are automatically bound to function keys provided that "set_key" hasn't been used to redefine the behaviour of the respective key.
*If you have a script that modifies the representation of the molecules and stores them, quickly, then the stored frames may not be up to date. I suggest calling "refresh" between the commands.

===SEE ALSO===
[[Cmd view]], [[Cmd set_view]], [[Cmd get_view]] [[Movie_from_scenes]]

===DEVELOPMENT TO DO===
Add support for save/restore of a certain global and object-and-state specific settings, such as: state, surface_color, ribbon_color, stick_color, transparency, sphere_transparency, etc. This would probably best be done by defining a class of "scene" settings which are treated in this manner. The current workaround is to create separate objects which are enabled/disabled differentially.

[[Category:Commands|scene]]
[[Category:States]]

Movie from scenes

2009-06-03T15:04:09Z

Harijay: Created page with 'From Pymol build 1.2 onwards , pymol allows you to build movies directly from scenes defined using the "Scene-Append menu item". To do this you will create the scenes combining t...'

From Pymol build 1.2 onwards , pymol allows you to build movies directly from scenes defined using the "Scene-Append menu item".
To do this you will create the scenes combining the views and representations you want and then use the command the command "Movie" - Program - Scene loop - Y rock , then pick a time for which the given scene should rock between camera interpolations .

This assumes that you have [http://freemol.org/ freemol] installed and configured and available on your path.
Failing which you can always save the images and make the movie externally. This very convenient functionality makes movie making a pretty WYSIWYG process.

To quote Warren from a recent pymol newsgroup post

''Assuming that you are using the most recent PyMOL 1.2 beta build, first create a Scene for each display you wish to show.

(To do that, show everything the way you want and then select “Append” from the “Scene” menu. Repeat the process for each view / color / representation you wish to show. You can PgUp / PgDown through defined Scenes.)

Then, to create the movie, select “Program -> Scene Loop -> Y-Rock -> # seconds each” from the “Movie” menu.

Now you can write out the movie as either a series of PNG files or an MPEG file using “Save Movie As…” from the “File” menu.
Using scenes to create movies is a lot easier than messing around with scripts : )!
Cheers,
Warren''

Gallery

2008-06-11T17:17:55Z

Harijay:

{| align="center"
|+ style="width: 90%; font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px; colspan:4" | PyMOLWiki Gallery
|- style="text-align:center; font-weight: bold; font-size:120%; color:#333;"
| Cool PyMOL-generated Images and their Scripts. ''[[Talk:Gallery#Adding|Add Your Own]]''
|}

{{GalleryImage
|image=Gm2.png|size=200px|title=Grid Mode|description=This image shows [[Grid mode|Grid Mode]] in action.
|cmdString=<source lang="python">
fetch 1cll 1sra 1ggz 5pnt 1rlw 1cdy;
set grid_mode
</source>
|seeAlso=
*[[Fetch]]
*[[Set]]
*[[grid_mode]]
}}

{{GalleryImage
|image=Fov60.png|size=200px|title=Cool Perspective|description=This image shows a perspective through [[Field_Of_View]].
|cmdString=<source lang="python">
load prot.pdb;
zoom i. 46-49 and n. CA
set field_of_view, 60
ray
</source>
|seeAlso=
*[[Load]]
*[[Ray]]
*[[Zoom]]
*[[Set]]
*[[Property_Selectors |Short form Selectors]]
}}

{{GalleryImage
|image=Pocket.png|size=200px|title=Representing a binding pocket|description=This image shows a nice way to show binding surfaces
|cmdString=<source lang="python">
load $TUT/1hpv.pdb, tmp
extract lig, organic
extract prot, polymer
delete tmp

set surface_carve_cutoff, 4.5
set surface_carve_selection, lig
set surface_carve_normal_cutoff, -0.1

show surface, prot within 8 of lig
set two_sided_lighting
set transparency, 0.5
show sticks, lig
orient lig

set surface_color, white
set surface_type, 2 # mesh
unset ray_shadows
</source>
|seeAlso=
*[[extract]]
*[[delete]]
*[[show]]
*[[set]]
*[[orient]]
*[[surface_carve_cutoff]]
*[[surface_carve_selection]]
*[[surface_carve_normal_cutoff]]
*[[surface_color]]
*[[surface_type]]
}}

Cartoon Helix Settings

2008-05-16T20:47:36Z

Harijay:

==Overview==
This setting sets the style in which [[Cartoon|cartoon]] helices are rendered. The default is a helix with an ellipsoid cross section. '''Fancy''' mode helices are ribbons with tubular edges à la [[MolScript]]. Cylindicial mode renders helices as solid cylinders.

==Syntax==
To turn on Fancy Helices:
set cartoon_fancy_helices, 1

To turn on Cylindrical Helices:
set cartoon_cylindrical_helices, 1

To return to default helices:
set cartoon_fancy_helices, 0
set cartoon_cylindrical_helices, 0

==Result==
<gallery>
image:Fancy.JPG|Fancy helix|center
image:Cylindre.JPG|Cylindrical helix
image:default.JPG|Default representation
</gallery>

==Change size of default cartoon helix==
To change the size of the cartoon helices when not in the fancy helix mode you change the dimensions of the oval that represents the cross section of the default cartoon representation.

[[Image:Cartoon_oval_length.png]]

set cartoon_oval_length , 0.8 # default is 1.20
and
set cartoon_oval_width , 0.2 # default is 0.25

Also see [[Cartoon_oval_width]] and [[Cartoon_oval_length]]
[[Category:Settings|Cartoon helix settings]]

Cartoon Helix Settings

2008-05-16T20:46:34Z

Harijay:

==Overview==
This setting sets the style in which [[Cartoon|cartoon]] helices are rendered. The default is a helix with an ellipsoid cross section. '''Fancy''' mode helices are ribbons with tubular edges à la [[MolScript]]. Cylindicial mode renders helices as solid cylinders.

==Syntax==
To turn on Fancy Helices:
set cartoon_fancy_helices, 1

To turn on Cylindrical Helices:
set cartoon_cylindrical_helices, 1

To return to default helices:
set cartoon_fancy_helices, 0
set cartoon_cylindrical_helices, 0

==Result==
<gallery>
image:Fancy.JPG|Fancy helix|center
image:Cylindre.JPG|Cylindrical helix
image:default.JPG|Default representation
image:Cartoon_oval_length.png|Cartoon Helix dimensions
</gallery>

== Change size of default cartoon helix ==
To change the size of the cartoon helices when not in the fancy helix mode you change the dimensions of the oval that represents the cross section of the default cartoon representation.

[[Image:Cartoon_oval_length.png]]

set cartoon_oval_length , 0.8 # default is 1.20
and
set cartoon_oval_width , 0.2 # default is 0.25

Also see [[Cartoon_oval_width]] and [[Cartoon_oval_length]]
[[Category:Settings|Cartoon helix settings]]

Cartoon oval width

2008-05-16T20:35:53Z

Harijay:

== Overview ==

Only relevant when oval (default) helices is turned on, see [[Cartoon_Helix_Settings]] 
set cartoon_oval_width defines the width of the helix 

== Syntax ==

<source lang="python">set cartoon_oval_width, <number> #default setting is 0.25</source>

== Example ==
<gallery>
Image:cartoon_oval_width_0.01.png|cartoon_oval_width 0.01
Image:cartoon_oval_width_default.png|cartoon_oval_width 0.2
Image:cartoon_oval_width_1.png|cartoon_oval_width 1
</gallery>

For editing the "length" of the ribbon see [[Cartoon_oval_length]]

[[Category:Settings|Cartoon oval width]]

PyMOL mailing list

2008-05-13T00:55:43Z

Harijay: New page: You can search the PyMol users mailing list using the mail search hosted at sourceforge [http://sourceforge.net/search/?ml_name=pymol-users&type_of_search=mlists&group_id=4546 Pymol user...

You can search the PyMol users mailing list using the mail search hosted at sourceforge

[http://sourceforge.net/search/?ml_name=pymol-users&type_of_search=mlists&group_id=4546 Pymol users mailing list search]

Search pymol-users mailing list

2008-05-13T00:55:43Z

Search Pymol source

2008-05-12T22:25:07Z

Harijay:

===Using krugle to search within pymol source===
You can use the krugle search engine and snoop around inside the pymol source.
[http://sourceforge.krugle.com/kse/projects/9WpYoax#7 Krugle python code search]
Use [http://sourceforge.krugle.com/kse/projects/9WpYoax this link] , click on the C, Python and other links in the section on the right , to be taken to a code search page. ( see image below)

[[Image:Code_search_links.png]]

[[Image:Stick_radius_code_search.png]]

File:Stick radius code search.png

2008-05-12T22:24:10Z

Harijay: A typical code search result using the krugle code search of sourceforge PyMol codebase

A typical code search result using the krugle code search of sourceforge PyMol codebase

Search Pymol source

2008-05-12T22:18:16Z

Harijay:

File:Code search links.png

2008-05-12T22:15:15Z

Harijay: The krugle code search engine indexes all sourceforge projects. You can search within pymols source using the highlighted links

The krugle code search engine indexes all sourceforge projects. You can search within pymols source using the highlighted links

Search Pymol source

2008-05-12T22:14:27Z

Harijay:

===Using krugle to search within pymol source===
You can use the krugle search engine and snoop around inside the pymol source.
[http://sourceforge.krugle.com/kse/projects/9WpYoax#7 Krugle python code search]
In the link above , click on the C, Python and other links in the section on the right , to be taken to a code search page. ( see image below)

Search Pymol source

2008-05-12T22:02:04Z

Harijay: New page: ===Using krugle to search within pymol source=== You can use the krugle search engine and snoop around inside the pymol source. [http://sourceforge.krugle.com/kse/projects/9WpYoax#7 Krugle...

Cartoon Helix Settings

2008-05-09T01:49:55Z

Harijay:

==Overview==
This setting sets the style in which [[Cartoon|cartoon]] helices are rendered. The default is a helix with an ellipsoid cross section. '''Fancy''' mode helices are ribbons with tubular edges à la [[MolScript]]. Cylindicial mode renders helices as solid cylinders.

==Syntax==
To turn on Fancy Helices:
set cartoon_fancy_helices, 1

To turn on Cylindrical Helices:
set cartoon_cylindrical_helices, 1

To return to default helices:
set cartoon_fancy_helices, 0
set cartoon_cylindrical_helices, 0

To change the size of the cartoon helices when not in the fancy helix mode
set cartoon_oval_radius , 0.8
and
set cartoon_oval_width , 0.2

==Result==
<gallery>
image:Fancy.JPG|Fancy helix|center
image:Cylindre.JPG|Cylindrical helix
image:default.JPG|Default representation
image:Cartoon_oval_length.png|Cartoon Helix dimensions
</gallery>

[[Category:Settings|Cartoon helix settings]]

File:Cartoon oval length.png

2008-05-09T01:44:51Z

Harijay: The cartoon helix dimensions are specified by the size of the oval crosssection.

The cartoon helix dimensions are specified by the size of the oval crosssection.

Cartoon Helix Settings

2008-05-09T01:42:10Z

Harijay:

==Overview==
This setting sets the style in which [[Cartoon|cartoon]] helices are rendered. The default is a helix with an ellipsoid cross section. '''Fancy''' mode helices are ribbons with tubular edges à la [[MolScript]]. Cylindicial mode renders helices as solid cylinders.

==Syntax==
To turn on Fancy Helices:
set cartoon_fancy_helices, 1

To turn on Cylindrical Helices:
set cartoon_cylindrical_helices, 1

To return to default helices:
set cartoon_fancy_helices, 0
set cartoon_cylindrical_helices, 0

To change the size of the cartoon helices when not in the fancy helix mode
set cartoon_oval_radius , 0.8
and
set cartoon_oval_width , 0.2

==Result==
<gallery>
image:Fancy.JPG|Fancy helix|center
image:Cylindre.JPG|Cylindrical helix
image:default.JPG|Default representation
</gallery>

[[Category:Settings|Cartoon helix settings]]