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{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"
|+ style="font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki
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| We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL].
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|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
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{| 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;"
{| align="center" style="width:90%; margin-bottom: 20px"
|+ 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
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{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
| 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-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
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| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to [[Special:Userlogin|join]]. Feel free to add any appropriate content; make an account and [[PyMolWiki:Community_Portal|get started]]!
| 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]]'''
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| 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]]'''
|}
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{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
 
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
{| width="100%"
| 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
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|-
| [[TOPTOC|'''Table of Contents''']]
! Official Release
|| [[Special:Allpages|Index of all pages]]
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
|-
|-
| [[:Category:Tutorials|Tutorials]]
! New Plugin
|| [[:Category:Commands|Commands]]
| [[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
|| '''Settings''': [[Settings|All]] | [[:Category:Settings|Documented]]
|-
|-
| [[:Category:Script_Library|'''Script Library''']]
! Official Release
|| [[:Category:Plugins|'''Plugins''']]
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|| [[:Special:Categories| See All Categories]]
|-
|-
| [[:Category:FAQ|Frequently Asked Questions]]
! Python 3
|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|| [[About| '''About PyMOL''']]
|-
|-
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! POSF
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|}
 
{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
|+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]])
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Added a starter gallery of PyMOL-created Journal [[Covers]].
! Selection keywords
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].
! 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
|-
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Downtime: The PyMOLWiki underwent some downtime due to FS problems.  There are also upgrades planned for this week, so we may expect a little downtime for that.  We've been <b>very</b> fortunate to have hosting from [http://www.bitgnome.net/ BitGnome.Net]; they've done an incredible job!
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[Gallery]] -- Did you make a [[:Image:Ccp4_map.png|cool image]]?  Pop it into the PyMOLWiki Gallery with the PyMOL command you used.  Looking for a particular representation--start here (new!).
! Older News
|}
| See [[Older_News|Older News]].
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:070920nature.pdf.jpg|155px]] Sample Cover from the [[Covers]] gallery.
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{| 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...
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category=Commands|Plugins|Script_Library|Settings
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includepage=*
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
escapelinks=false
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allowcachedresults=false
| style="padding: 3px 5px 10px 15px;"| &diams; PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
resultsheader=__NOTOC__ __NOEDITSECTION__
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listseparators=,<h3>[[%PAGE%]]</h3>,,\n
| style="padding: 3px 5px 10px 15px;"| &diams; [[group]] command has been added.
</DynamicPageList>
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</div>
| style="padding: 3px 5px 10px 15px;"| &diams; The truly awesome [[grid_mode]] setting has been added.
<div style="clear: both;"></div>
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| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|125px]] Screenshot of [[grid_mode|Grid Mode]] in action.
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{|style="background-color: transparent;" width="100%"
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts &amp; Plugins
escapelinks=false
|-
openreferences=true
| style="padding: 3px 5px 10px 15px;"| &diams; Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
|-
ordermethod=none
| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!
allowcachedresults=false
|-
</DynamicPageList>
| style="padding: 3px 5px 10px 15px;"| &diams; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
 
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added.  Catalytic site prediction, other tools.  Redirects to website.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[EMovie]] plugin added.  Easy movies in PyMol using a GUI.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[DYNMAP]] plugin page created.  Check it out!
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| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
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|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:COLORAMA-screenshot.jpg|125px]] Screenshot of [[Colorama]].
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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...

Pdb conect all

When saving a PDB file, the pdb_conect_all settings controls whether PyMOL writes CONECT records for all bonds, or only for HETATM bonds.

PDB files by convention do not contain bond information for standard polymer residues (ATOM records), because the connectivity is known for those.

If a PDB file contains at least one CONECT record for two atoms from ATOM records, then PyMOL will set pdb_conect_all=on as an object-level setting, to again write CONECT records for all bonds when saving that object to a PDB file.

Values

  • off turns the feature off, CONECT records are written for HETATM bonds only
  • on turns the feature on, CONECT records are written for all bonds

Example

The PDB file for 1rx1 contains 52 CONECT records (for the ligands). 

fetch 1rx1, async=0
set pdb_conect_all, on
save 1rx1_conect_all.pdb

Now the file 1rx1_conect_all.pdb contains 1316 CONECT records.

See Also
A Random PyMOL-generated Cover. See Covers.


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