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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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== [[Initial Wiki Layout Suggestion]] == (Warren Delano)
{| 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;"
* [[Mouse Controls]]
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== [[User Additions]] ==
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* [[NMR Applicaitons]] (Doug Kojetin)
| style="vertical-align: top; width: 40%" |
* [[Plugins/Modules]] (Doug Kojetin)
{| class="jtable" style="float: left; width: 90%;"
** [[APBS Plugin]]
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
----
|-
* [[Plugins]] (Michael George Werner)
! New Setup
** [[List of Plugins]]
| [https://github.com/kullik01/pymol-open-source-windows-setup/releases/tag/v3.1.0 PyMOL-open-source-windows-setup v3.1] has been released on January 20, 2025. More information under [[Windows Install]].
** [[Tutorial on writing plugins]]
|-
** [[Others]]
! New Plugin
----
| [[PySSA]] aims to combine PyMOL and [https://github.com/sokrypton/ColabFold ColabFold] to enable the prediction and analysis of 3D protein structures for the scientific end-user. [https://github.com/urban233/PySSA/releases/tag/v1.0.1 v1.0 has been released] on July 10, 2024.
* [[Structure Alignment]] (Nat Echols)
|-
** [[Structure Alignment Editor]]
! Official Release
* [[3rd Party Applications]]
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
** [[Movies]]
|-
** [[Codecs]]
! 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]].
|}
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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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|}
02:06, 16 Feb 2005 (CST)
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Latest revision as of 13:01, 21 January 2025

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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
New Setup PyMOL-open-source-windows-setup v3.1 has been released on January 20, 2025. More information under Windows Install.
New Plugin PySSA aims to combine PyMOL and ColabFold to enable the prediction and analysis of 3D protein structures for the scientific end-user. v1.0 has been released on July 10, 2024.
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...

Set name

set_name can be used to change the name of an object or selection.

Not only can you simply rename an object or selection, but this command is also a powerful tool for those who deal with multiple structures in one file --- say a collection of NMR models. The user can execute the Split_States command and then rename the molecule of choice in the state of choice. For example, if one loads an NMR structure (with, say, 20 states) and aligns it to another structure, the balance of the alignment will (most likely) be off due to the weighting of the 19 other structures you probably don't see. To overcome this problem, one simply executes Split_States and then renames one of the states and then aligns that newly renamed object.

USAGE

set_name old_name, new_name

PYMOL API

cmd.set_name(string old_name, string new_name)


User Comments/Examples

cmd.set_name("example", "nicename")

As the order of arguments is different from, for example, the ..→

A Random PyMOL-generated Cover. See Covers.


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