Symmetry

2020-11-17T16:10:19Z

Bosmith: /* https://pymolwiki.org/index.php/Symexp */

2011-02-03T15:48:50Z

Bosmith: /* Example 1 - starting with a complex in a single files */

'''get_area''' calculates the surface area in square Angstroms of the selection given. Note that the accessibility is assessed in the context of the object(s) that the selection is part of. So, to get the surface areas of e.g. a component of a complex, you should make a new object containing a copy of just that component and calculate its area.

===USAGE===
<source lang="python">
get_area sele [,state[, load_b ]]
</source>

===PYMOL API===
<source lang="python">
cmd.get_area(string selection="(all)", load_b=0, state=0 )
</source>

= Examples =
== Example 1 - starting with a complex in a single file ==
<source lang="python">
# load complex
# Haemoglobin in this example illustrates careful use of selection algebra
load 2HHB.pdb

# create objects for alpha1, beta1 and alpha1,beta1 pair of subunits
create alpha1, 2HHB and chain A
create beta1, 2HHB and chain B
create ab1, 2HHB and chain A+B

# get hydrogens onto everything (NOTE: must have valid valences on e.g. small organic molecules)
h_add

# make sure all atoms within an object occlude one another
flag ignore, none

# use solvent-accessible surface with high sampling density
set dot_solvent, 1
set dot_density, 3

# measure the components individually storing the results for later
alpha1_area=cmd.get_area("alpha1")
beta1_area=cmd.get_area("beta1")

# measure the alpha1,beta1 pair
ab1_area=cmd.get_area("ab1")

# now print results and do some maths to get the buried surface
print alpha1_area
print beta1_area
print ab1_area
print (alpha1_area + beta1_area) - ab1_area
</source>

== Example 2 - starting with two components in separate files ==
<source lang="python">
# load components separately
load my_ligand.pdb
load my_target.pdb

# get hydrogens onto everything (NOTE: must have valid valences on the ligand...)
h_add

# make sure all atoms within an object occlude one another
flag ignore, none

# use solvent-accessible surface with high sampling density
set dot_solvent, 1
set dot_density, 3

# measure the components individually
ligand_area=cmd.get_area("my_ligand")
target_area=cmd.get_area("my_target")

# create the complex
create my_complex, my_ligand my_target

# measure the complex
complex_area=cmd.get_area("my_complex")

# now print results
print ligand_area
print target_area
print complex_area
print (ligand_area + target_area) - complex_area
</source>

==Example 3 - using load_b to get surface area per atom ==
<source lang="python">
# example usage of load_b
# select some organic small molecule
select ligand, br. first organic
# get its area and load it into it's b-factor column
get_area ligand, load_b=1
# print out the b-factor/areas per atom
iterate ligand, print b
</source>

== See Also ==
* For an example of '''load_b''' in use check out [[FindSurfaceResidues]].
* [[Surface]], most notably [[Surface#Calculating_a_partial_surface]].

[[Category:Commands|Get Area]]
[[Category:Biochemical_Properties|Get Area]]

Get Area

2011-02-03T15:28:49Z

Bosmith:

'''get_area''' calculates the surface area in square Angstroms of the selection given. Note that the accessibility is assessed in the context of the object(s) that the selection is part of. So, to get the surface areas of e.g. a component of a complex, you should make a new object containing a copy of just that component and calculate its area.

===USAGE===
<source lang="python">
get_area sele [,state[, load_b ]]
</source>

===PYMOL API===
<source lang="python">
cmd.get_area(string selection="(all)", load_b=0, state=0 )
</source>

= Examples =
== Example 1 - starting with a complex in a single files ==
<source lang="python">
# load complex
# Haemoglobin in this example illustrates careful use of selection algebra
load 2HHB.pdb

# create objects for alpha1, beta1 and alpha1,beta1 pair of subunits
create alpha1, 2HHB and chain A
create beta1, 2HHB and chain B
create ab1, 2HHB and chain A+B

# get hydrogens onto everything (NOTE: must have valid valences on the ligand...)
h_add

# make sure all atoms within an object occlude one another
flag ignore, none

# use solvent-accessible surface with high sampling density
set dot_solvent, 1
set dot_density, 3

# measure the components individually storing the results for later
alpha1_area=cmd.get_area("alpha1")
beta1_area=cmd.get_area("beta1")

# measure the alpha1,beta1 pair
ab1_area=cmd.get_area("ab1")

# now print results and do some maths to get the buried surface
print alpha1_area
print beta1_area
print ab1_area
print (alpha1_area + beta1_area) - ab1_area
</source>

== Example 2 - starting with two components in separate files ==
<source lang="python">
# load components separately
load my_ligand.pdb
load my_target.pdb

# get hydrogens onto everything (NOTE: must have valid valences on the ligand...)
h_add

# make sure all atoms within an object occlude one another
flag ignore, none

# use solvent-accessible surface with high sampling density
set dot_solvent, 1
set dot_density, 3

# measure the components individually
ligand_area=cmd.get_area("my_ligand")
target_area=cmd.get_area("my_target")

# create the complex
create my_complex, my_ligand my_target

# measure the complex
complex_area=cmd.get_area("my_complex")

# now print results
print ligand_area
print target_area
print complex_area
print (ligand_area + target_area) - complex_area
</source>

==Example 3 - using load_b to get surface area per atom ==
<source lang="python">
# example usage of load_b
# select some organic small molecule
select ligand, br. first organic
# get its area and load it into it's b-factor column
get_area ligand, load_b=1
# print out the b-factor/areas per atom
iterate ligand, print b
</source>

== See Also ==
* For an example of '''load_b''' in use check out [[FindSurfaceResidues]].
* [[Surface]], most notably [[Surface#Calculating_a_partial_surface]].

[[Category:Commands|Get Area]]
[[Category:Biochemical_Properties|Get Area]]

Get Area

2011-02-03T15:08:04Z

Bosmith:

Stereo 3D Display Options

2010-12-02T16:32:48Z

Bosmith: /* 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)===

* [http://www.engadget.com/2008/08/26/viewsonic-shows-off-a-120hz-lcd-display-for-computers ViewSonic VX2265wm] (VX2268wm in Europe) - [http://www.google.com/products?q=ViewSonic%20VX2265wm&btnG=Search+Froogle&lmode=unknown On the market] and [http://sourceforge.net/mailarchive/forum.php?thread_name=DED5C399-7534-4D3D-8B19-E3676C4F1867%40weizmann.ac.il&forum_name=pymol-users verified working under FC 12]

* [http://www.nvidia.com/object/product_GeForce_3D_VisionBundle_us.html Samsung 2233RZ] - On the market. Quad buffered stereo in Linux 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 (currently, the cheapest card that works in Linux is the Quadro FX 3700), 195.22 (or newer) nvidia linux binary driver, and the Nvidia 3d vision kit. Even though the Quadro FX 1400/3450/4000 cards have a 3 pin stereo connector, these will not work with Nvidia 3D vision since these have core versions less than G8x. For more information see this forum post [http://forums.nvidia.com/index.php?showtopic=91072&view=findpost&p=968627 at the Nvidia Forums]. - SP

* 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

* The 195.22 Nvidia linux drivers do not support the Samsung 2233RZ in Stereo mode 3 or 10 for quad buffered stereo with other stereo kits, emitters, or goggles such as those purchased from NuVision, Stereographics, or Edimensional. You cannot use NuVision, Stereographics, or Edimensional goggles with the Nvidia 3D Vision emitters. - SP

* 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.

==== NVidia NVision 3D Setup ====
The NVidia 3D NVision setup provides a very nice 3D experience. You need the following to enable PyMOL to show NVision 3D on Windows. Please review the hardware and software requirements before moving on to the installation and setup.

=====Necessary Hardware=====
* Monitor: 120 Hz LCD: a [http://www.samsung.com/us/consumer/office/monitors/specialty/LS22CMFKFV/ZA/index.idx?pagetype=prd_detail&returnurl=|Samsung 2233RZ] or a [http://www.viewsonic.com/products/desktop-monitors/lcd/x-series/vx2265wm-fuhzion-lcd.htm|ViewSonic Fuhzion vx2265wm]
* Cable: [http://images.google.com/imgres?imgurl=http://www.logicsupply.com/images/dvi_connector_types.gif&imgrefurl=http://www.logicsupply.com/faq&usg=__G2BLaVTqBN4ie8fz_LJR1zc3zBc=&h=261&w=440&sz=15&hl=en&start=0&sig2=_hFM6ICIsxPq5WIAv8BCqg&zoom=1&tbnid=NIcKIs_BW_2rmM:&tbnh=135&tbnw=228&ei=KHN2TL-UC8P_lgfr44nsCw&prev=/images%3Fq%3Ddual%2Blink%2Bdvi%26hl%3Den%26biw%3D1475%26bih%3D1042%26gbv%3D2%26tbs%3Disch:1&itbs=1&iact=hc&vpx=136&vpy=323&dur=3153&hovh=173&hovw=292&tx=227&ty=74&oei=KHN2TL-UC8P_lgfr44nsCw&esq=1&page=1&ndsp=30&ved=1t:429,r:6,s:0 Dual Link DVI cable]; most 120Hz monitors will come with this cable--regardless, the cable is necessary
* Quadro Card: recent [http://www.nvidia.com/page/quadrofx_family.html Quadro] series graphics card (not a GeForce card) such as an FX 380 or 570 or later. The GeForce cards do not support windowed openGL stereo, so we do not support these series of cards for the NVision 3D solution
** '''WARNING''': The Quadro FX1400 does not support stereo on Windows7
* Emitter: [http://www.nvidia.com/object/3d-vision-main.html|GeForce 3D Vision] hardware kit (an emitter with 3D shutter glasses)

=====Necessary Software=====
* Windows XP 32 bit (testing other OSs soon!), Windows Vista
* Latest Quadro [http://www.nvidia.com/Download/index.aspx?lang=en-us|Graphics Drivers from NVidia].
* Latest [http://www.nvidia.com/Download/index.aspx?lang=en-us|3D Graphics drivers for the NVision system]--under '''Product Type''' choose '''3D Vision'''.

=====Installation Instructions=====
======System Setup======
# Install the Quadro '''Graphics Drivers''' and reboot your machines
# Install the NVision Installation, hooking up the 3D emitter and glasses as directed in the instructions
## Make sure the 3D demos work
## Complete the '''3D Vision Drivers''' install (I had errors/warnings about old drivers but this did't matter)
# Specify how to drive the 3D by, click on
:::'''Windows Start Button''' > '''Control Panel''' > '''NVidia Control Panel''' > '''Manage 3D Settings''' (tab) > '''Global Settings''' (tab on the right) > '''Base Profile''' (tab). Then, under '''Settings''' choose '''Stereo - Display Mode'''. Next, select '''Generic Active Stereo (with NVidia IR Emitter)'''. If you have a DLP monitor/TV choose the corresponding DLP option. You '''must''' also set '''Stereo - Enable''' to '''on'''.

======Running PyMOL======
That's it! PyMOL should now work in Quad Buffered 3D Stereo using the NVidia 3D NVision system. To run PyMOL in 3D mode on:
*Windows
:: '''Start > PyMOL > PyMOL > PyMOL 3D Launch (last menu option) > PyMOL Stereo (Quad Buffered 3D)'''
*Linux
:: pymol -s -t 1
* Mac
:: Sorry, at this time the NVision system is not known to work on Macs.

=== 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.zalman.co.kr/Eng/product/Product_Read.asp?idx=391 Zalman 24-inch 3D LCD monitor] - also works with PyMOL 1.2b3 & later under LINUX (Centos 5 x86_64 plain kernel + NVidia driver from ELRepo). I'm using an NVidia Quadro FX 580 (G96GL) graphics card (was £125) with

Option "Stereo" "7"

in the Screen section of xorg.conf and an additional

Section "Extensions"
Option "Composite" "Disable"
EndSection

Monitor cost around £350. PyMOL automagically detects that quad buffered stereo is available on startup.--[[User:Bosmith|Bosmith]] 16:32, 2 December 2010 (UTC)
* [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]]

Displaying Biochemical Properties

2007-10-05T13:04:53Z

Bosmith: /* Hydrogen bonds where find->polar contacts doesn't do what you need */

==Selecting secondary structures==
A few examples:
<source lang="python">
select helix, (ss h)
select sheet, (ss s)
select loop, (ss l+'')
</source>

===Manually Assigning Secondary Structure===
You can manually assign secondary stuctures to your protein by

<pre>
alter 96-103/, ss='S'
alter 96-103/, ss='H'
alter 96-103/, ss='L'</pre>

to set residues 96-103 to beta Strand, alpha Helix, and Loop respectively.

===See Also===
[[Cmd dss]]

[[:Category:FAQ|FAQ]] [[:Category:Objects_and_Selections|Displaying Biochemical Properties]]

==Color by atom type from a script==
See [[Color]] for this.

==Displaying double bonds==
You can go into the lines mode and turning on the valence display:
<source lang="python">
hide
show lines
set valence, 0.1
</source>

A higher value for valence spreads things out more. I don't know of a way to get the dotted notation.

==Calculating dihedral angles==
The get_dihedral function requires four single-atom selections to work:
<source lang="python">
get_dihedral prot1///9/C, prot1///10/N, prot1///10/CA, prot1///10/C
</source>

==Hydrogen bonds and Polar Contacts==
[[Image:Polar_contacts_small.png|thumb|Polar Contacts in PyMol|center|300px]]
Using the actions [A] button for an object or selection you can display Hydrogen bonds and Polar Contacts.
[A]->find->polar contacts-><select from menu>

The command behind the menus is the <b>dist</b>ance command called with the additional argument mode=2.

Parameters that control the the identification of H-bonds are defined as
set h_bond_cutoff_center, 3.6
with ideal geometry and
set h_bond_cutoff_edge, 3.2
with minimally acceptable geometry.

These settings can be changed *before* running the detection process (dist
command mode=2 or via the menus).

Note that the hydrogen bond geometric criteria used in PyMOL was designed to
emulate that used by DSSP.

=== Hydrogen bonds between specific atoms ===
<source lang="python">
dist name, sele1, sele2, mode=2
</source>

=== Hydrogen bonds where find->polar contacts doesn't do what you need ===
You can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use [[h_add]] on the proteins, or provide ligands with valence information and then use h_add.

Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens.
<source lang="python">
# EXAMPLE 1: Show hydrogen bonds between protein
# and docked ligands (which must have hydrogens)

load target.pdb,prot
load docked_ligs.sdf,lig

# add hydrogens to protein

h_add prot

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (lig and acc),(prot and don), 3.2
dist HBD, (lig and don),(prot and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD
</source>
<source lang="python">
# EXAMPLE 2
# Show hydrogen bonds between two proteins

load prot1.pdb
load prot2.pdb

h_add prot1
h_add prot2

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (prot1 and acc),(prot2 and don), 3.2
dist HBD, (prot1 and don),(prot2 and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# NOTE: that you could also use this approach between two
# non-overlapping selections within a single object.
</source>
There is also a [http://www.ebi.ac.uk/~gareth/pymol/downloads/scripts/hbond.py script] drawing nice hydrogen bonds from [http://www.ebi.ac.uk/~gareth Gareth Stockwell].

The "polar contacts" mentioned above are probably better at finding hydrogen bonds than these scripts. "Polar contacts" check geometry as well as distance.

==Assign color by B-factor==
See section [[Color]] for this.

==Polar surface area==
For a solvent accessible PSA approximation:
<source lang="python">
set dot_density, 3
remove hydro
remove solvent
show dots
set dot_solvent, on
get_area elem N+O
get_area elem C+S
get_area all
</source>

For molecular PSA approximation
<source lang="python">
set dot_density, 3
remove hydro
remove solvent
set dot_solvent, off
get_area elem N+O
get_area elem C+S
get_area all
</source>

Showing dots isn't mandatory, but it's a good idea to confirm that you're getting the value for the atom dot surface you think you're using.
Please realize that the resulting numbers are only approximate, reflecting the sum of partial surface areas for all the dots you see. To increase accuracy, set dot_density to 4, but be prepared to wait...

==Display solvent accessible surface==
Using the surface display mode, PyMOL doesn't show the solvent accessible surface, rather it shows the solvent/protein contact surface. The solvent accessible surface area is usually defined as the surface traced out by the center of a water sphere, having a radius of about 1.4 angstroms, rolled over the protein atoms. The contact surface is the surface traced out by the vdw surfaces of the water atoms when in contact with the protein.

PyMOL can only show solvent accessible surfaces using the dot or sphere representations:

for dots:
<source lang="python">
show dots
set dot_mode,1
set dot_density,3
</source>

for spheres:
<source lang="python">
alter all,vdw=vdw+1.4
show spheres
</source>

==Displaying the C-Alpha trace of proteins==
<source lang="python">
hide
show ribbon
set ribbon_sampling,1
</source>

And if your model only contains CA atoms, you'll also need to issue:
<source lang="python">
set ribbon_trace,1
</source>

==Displaying the Amino Acid Backbone==
The easiest way to see the backbone of the protein is to do
<source lang="python">
hide all
show ribbon
</source>

If you don't like the ribbon representation, you can also do something like
<source lang="python">
hide all
show sticks, name C+O+N+CA
</source>
You can replace '''sticks''' in the above by other representations like '''spheres''' or '''lines'''.

==Displaying the Phosphate backbone of nucleic acids==

====Native Nucleic Acid Rendering in PyMol====
PyMol now better supports viewing nucleic acid structure. [[Nuccyl]] still seems to be the reigning champ for image quality, but see PyMol's native [[Cartoon]] command.
----

Should you ever want to show the phosphate trace of a nucleic acid molecule:
<source lang="python">
def p_trace(selection="(all)"):
s = str(selection)
cmd.hide('lines',"("+s+")")
cmd.hide('spheres',"("+s+")")
cmd.hide('sticks',"("+s+")")
cmd.hide('ribbon',"("+s+")")
cmd.show('cartoon',"("+s+")")
cmd.set('cartoon_sampling',1,"("+s+")")
cmd.set('cartoon_tube_radius',0.5,"("+s+")")
cmd.extend('p_trace',p_trace)
</source>

and then:
<source lang="python">
p_trace (selection)
</source>

==Align proteins with CA fit==
If two proteins have significant homology, you can use the [[Cmd align]] command:
<source lang="python">
align prot1////ca,prot2
</source>

which will perform a sequence alignment of prot1 against prot2, and then an optimizing fit using the CA positions. I'm not sure if the help text for align got into 0.82, but the next version will definitely have it.

[[Category:Objects_and_Selections|Displaying Biochemical Properties]]

Cmd h add

2007-10-05T13:03:54Z

Bosmith: Cmd h add moved to H add

#REDIRECT [[H add]]

H Add

2007-10-05T13:03:54Z

Bosmith: Cmd h add moved to H add

"h_add" uses a primitive algorithm to add hydrogens onto a molecule.

<b>menus</b>
[A]->hydrogens->add

<b>command line/console</b>
<source lang="python">
h_add (selection)
</source>

<b>via python API</b>
<source lang="python">cmd.h_add( string selection="(all)" )</source>

see also [[h_fill]]

[[Category:Commands|h]]

H Add

2007-10-05T11:18:30Z

Bosmith:

H Add

2007-10-05T11:16:43Z

Bosmith:

H Add

2007-10-05T11:16:34Z

Bosmith:

2006-08-04T08:21:22Z

Bosmith:

A recipe for reading surfaces from Roman Laskowski's SURFNET program (for finding cavities in macromolecules) into PyMol for visualisation.

Create your surfaces in "CCP4" format in SURFNET.

Aside: SURFNET can be compiled against ccp4 version 5 and 6 libraries by following the instructions in the SURFNET distribution and modifiying the link lines at the end of ccp4link.scr to replace

$CLIB/libccp4.a

with

$CLIB/libccp4f.a $CLIB/libccp4c.a