Difference between revisions of "Main Page"

Latest revision as of 12:54, 12 March 2024

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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
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...
Get chains This command will return a python list of chains for the given selection. Proteins structures often have more than one chain of residues present in a structure file. This command will fetch the names of each chain present. Because of the lack of standards, sometimes chain A will also be blank "". This isn't a problem for PyMOL, but be warned sometimes you may get back, [""]. Syntax # using get_chains for the object or selection called objSel get_chains objSel Examples # examples fetch 1cll print "1CLL has the following chains:", cmd.get_chains("1cll") # list all chains in all proteins loaded in PyMOL: for x in cmd.get_names(): for ch in cmd.get_chains(x): print x, " has chain ", ch See Also Get_Names

A Random PyMOL-generated Cover. See Covers.

Difference between revisions of "Main Page"

Latest revision as of 12:54, 12 March 2024

Get chains

Syntax

Examples

See Also

Navigation menu

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-== PyMol Wiki Home ==
+__NOTOC__
-You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.
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-We provide
+|}
-* updates on [http://pymol.sf.net PyMol]
+{| align="center" style="padding-bottom: 3em;"
-* a stable user-oriented documentation base
+|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
-* a thorough treatment of the PyMol program
+|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
-* feature-rich scripts for general PyMol use
+| 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;"
-==News==
+| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
-* New PyMol Features: [[Examples_of_cartoon_ring_and_cartoon_ladder_settings|Nucleic Acid Representation Settings]] & Examples.
+|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
-* Cool new Plug-In: [[Show_NMR_constrains| Show NMR Constrains]].
+|}
-* Check out PyMol's new [[Cartoon#Nucleic_Acid_Representation|Nucleic Acid Rendering]]
-* Added [[DynoPlot]] script for plotting data within PyMol; an interactive Ramachandran plot.
-* Added [[Kabsch]] script for optimal alignment of two sets of vectors.
-* Some details have been released about [[0.99beta11]]'s release and new features.
-* A new map function is in the beta build, [[Map_Trim]].
-* Details on how to build [[Peptide_Sequence| peptide sequences]] and [[Nucleic_Acid_Sequence| nucleic acid sequences]] by hand.
-* New [[Transform_odb]] script to transform coordinates with .odb file from O or LSQMAN
-See our [[Older_News]].
-== Links of Interest ==
-* [[TOPTOC|Top Level Table of Contents]]
-* [[:Category:FAQ|Frequently Asked Questions]] -- new!
-* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
-* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
-* [[:Category:Commands|PyMol Commands]] (>130 documented!)
-* [[:Special:Allpages| All Pages]]
-* [[:Category:Plugins|Plugins]]
-* [[:Special:Categories| See All Categories]]
+{| 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;"
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+|-
+| 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]]'''
+|}
+{| 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 &amp; 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" >
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