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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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=== Helping ===
{| 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;"
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages.  We now need people to assist with
|+ 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]]'''
|}


* A wiki edit/user policy is needed.
{| width="100%"
* Wiki schema/design/organization: Below you'll find the current layout design
| style="vertical-align: top; width: 40%" |
* Graphic design and CSS layout: We need logos, BG images and CSS layout
{| class="jtable" style="float: left; width: 90%;"
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
* Etc...
|-
! 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>


=== Editors Needed ===
|}
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!
 
[[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:Discussion|Discussion]]
## [[:Category:PyMOL Beta|The Bleeding Edge]]
# [[Technical Issues]] (installation, hardware)
## [[Installation]]
### [[OS Dependent]]
#### [[Linux]]
#### [[MAC]]
#### [[Windows]]
# [[Using the GUI]]
## [[Launching PyMOL]]
### [[Command Line Options]]
### [[Launching From a Script]]
## [[Mouse Controls]]
## [[Objects and Selections]]
### [[Working with Objects]]
### [[Working with Selections]]
### [[Selector Quick Reference]]
#### [[Single-word Selectors]]
#### [[Property Selectors]]
#### [[Selection Algebra]]
#### [[Selection Macros]]
### [[Representations]]
#### [[Lines]]
#### [[Sticks]]
#### [[Cartoon]]
#### [[Surface]]
#### [[Mesh]]
#### [[Spheres]]
#### [[Dots]]
### [[Color]]
### [[Displaying biochemical properties]]
## [[Display Settings]]
## [[Stereo 3D Display]]
### [[Hardware Options]]
### [[Linux XFree86 Configuration]]
## [[Scenes]]
## [[Mouse Settings]]
## [[Wizards]]
## [[Plugins]]
## [[Ray-tracing]]
## [[Settings Reference (all settings and what they do)]]
## [[Movies and Animations]]
## [[Structure Alignment]]
## [[Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[PyMOL Command Script]]
## [[PyMOL Python API]]
# [[Advanced Issues]] (Ray tracing, settings)
## [[Launching PyMOL (has been asked often)]]
## [[Advanced Atom Selections]]
## [[Modeling and editing structures.]]
### [[Editing atoms]]
### [[Molecular sculpting]]
### [[Homology modeling]]
## [[Image Manipulation]]
### [[labels]]
### [[Photoshop/GIMP]]
### [[Stereo Figures]]
### [[Creating publication-quality images HOWTO]]
# [[Scripting]]
## [[Example Scripts]]
## [[Script Library]]
# [[:Category:Plugins|Plugins]]
## [[How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
## [[rtools Plugin]]
## [[Tutorial on writing plugins]]
## [[Others]]
# [[High-level applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
### [[Symmetry]]
### [[Electron Density]]
## [[NMR Applications]]
### [[Working with a Family of Structures]]
### [[Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
# [[3rd Party Software]]
## [[3rd Party Applications]]
### [[Movies]]
### [[Codecs]]
# [[Python Integration]]
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
## [[Arbitrary Graphics Objects]]
# [[Category: 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...

Pdbsurvey

Hi everyone !

I have created a script because I was tired of browsing the pdb for endless searches of structures relevant to my field. This scripts takes as input a text file in which you copied your favourite keywords, and the number of days you want to search back (by default, it will look at the structures added the last 50 days). It generates a report text file that contains the pdb id and name of the relevant structures that have been recently added. All you need to do is add 'run pdbsurvey.py' to your startup file, and create a text file called 'keywords.txt' with your keywords separated by an end-of-line character. Then you're ready to go. Just hit 'pdbsurvey' from within your PyMol instance, and the program returns the report file. The pdb ftp server is updated weekly.

<source lang="python"> from pymol import cmd

def pdbsurvey(days=50): 

   """USAGE : pdbsurvey (<days>)
   Surveys the updates added to the PDB (ftp.rcsb.org) in the last
   50 days (or otherwise specified when calling this function) for
   entries that  ..→
A Random PyMOL-generated Cover. See Covers.


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