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| == PyMol Wiki Home == | | __NOTOC__ |
| You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.
| | {| 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: 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/]] |
| 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;" |
| | |+ 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]]''' |
| | |} |
|
| |
|
| | {| 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 |
| | |- |
| | ! 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> |
|
| |
|
| | | |} |
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