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== PyMol Wiki Home ==
__NOTOC__
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.
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|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
|}
{| align="center" style="padding-bottom: 3em;"
|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
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=== Go! ===
{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
You may now add content to the wiki. This is a semi-structured wiki in that the categories are pseudo-hierarchically linked.
|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; border-bottom: 1px solid #fff;" |Quick Links
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[PyMOL_mailing_list|Getting Help]]'''
|}


=== New Categories/Content ===
{| width="100%"
If you feel we're missing a category, please find where it would most logically fit, add it to the main page via the [[Top Level Schema Policy]].
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
! New Plugin
| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
|-
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
! Selection keywords
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
! Plugin Update
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
|-
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! Older News
| See [[Older_News|Older News]].
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<DynamicPageList>
randomcount=1
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=1050
escapelinks=false
allowcachedresults=false
resultsheader=__NOTOC__ __NOEDITSECTION__
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</DynamicPageList>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<DynamicPageList>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
ordermethod=none
allowcachedresults=false
</DynamicPageList>


=== Helping ===
|}
* A wiki edit/user policy is needed.
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content:  We have (lots) of email to sift through, extract data from and import into the Wiki
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].
 
We need your help.  So join today & happy editing!
 
=== New! GeShi: Syntax Highlighting for Python & More ===
We now have a syntax highlighter installed.  It now supports something like 28 programming languages!  When you paste your code simply wrap it in
&lt;language_name&gt; ... code here ... &lt;/language_name&gt;. 
 
Here's an example:
<pre>
&lt;python&gt;
  # axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain
 
# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z
 
obj = [
  CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
  CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
  CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
  ]
 
# add labels to axes object (requires pymol version 0.8 or greater, I
# believe
 
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
 
# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
 
&lt;python&gt;
</pre>
 
gives us the code
<source lang="python">
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain
 
# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z
 
obj = [
  CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
  CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
  CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
  ]
 
# add labels to axes object (requires pymol version 0.8 or greater, I
# believe
 
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
 
# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</source>
 
See [http://qbnz.com/highlighter/index.php The Geshi Home Page]
 
[[User:Tree|Tree]]
 
== Section Layout ==
Please do not ADD any content to the site yet.  Just Organize the following list as logically as possible.  Here's my first go at it.
 
Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.
 
=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Plugins |Plugins]] -- wrong place?
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Latest revision as of 11:54, 12 March 2024

hosted by SBGridlogo2.jpg
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v3.0 has been released on March 12, 2024.
New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
Official Release PyMOL v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellowship announced for 2022-2023
Tutorial Plugins Tutorial updated for PyQt5
New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News See Older News.
Did you know...

FilterByMol

== Overview ==

This script filters through all the PDBs in the parent dir (you can easily the the directory it scans). For each molecule, it saves just the ligands/heteroatoms (excluding the waters). This gives you a simple way to filter through a database of proteins looking only at their ligands.

This script, as noted below, works on the objects at the level of a molecule. While we can iterate over atom number (ID), residue number (resi), etc we do not have any such "MOLID". So, we provide this simple workaround. You might need this file because if you have a residue (like #111 from 3BEP) that consists of a molecule and an atom then there's no other way to save the separate pieces (of molecule/atom) into two (or more files). As you can see in the following listing, if we iterate over the hetero atoms (and not waters) in 3BEP we get, <source lang="python"> PyMOL>iterate bymol het, print resi, resn, ID, chain, segi, alt 111 5CY 6473 C 111 5CY 6474 C 111 5CY 6476 C 111 5CY 6477 C 111 5CY 6478 C 111 5CY ..→

A Random PyMOL-generated Cover. See Covers.


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