Difference between revisions of "Main Page"

From PyMOLWiki
Jump to navigation Jump to search
(PyMOL 3.0 release)
 
(237 intermediate revisions by 24 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
−
{| align="center" width="90%"
+
{| 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
+
|+ 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/]]
−
|- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
+
|}
−
| We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL].
+
{| 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;"
 
|}
 
|}
  
−
 
+
{| 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
−
|
+
|-
−
{| 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
 
 
|-
 
|-
−
| 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]]'''
 
|-
 
|-
−
|}
+
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
−
{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
+
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
−
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
+
||'''[[PyMOL_mailing_list|Getting Help]]'''
−
|-
 
−
| [[TOPTOC|'''Table of Contents''']]
 
−
|| [[Special:Allpages|Index of all pages]]
 
−
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] [[CheatSheet|Wiki Page]]
 
−
|-
 
−
| [[:Category:Tutorials|Tutorials]]
 
−
|| [[:Category:Commands|Commands]]
 
−
|| '''Settings''': [[Settings|All]] [[:Category:Settings|Documented]]
 
−
|-
 
−
| [[:Category:Script_Library|'''Script Library''']]
 
−
|| [[:Category:Plugins|'''Plugins''']]
 
−
|| [[:Special:Categories| See All Categories]]
 
−
|-
 
−
| [[:Category:FAQ|Frequently Asked Questions]]
 
−
|| [[Gallery|'''Gallery''']]
 
−
|| [[About| '''About PyMOL''']]
 
−
|-
 
−
|}
 
−
|
 
 
|}
 
|}
  
−
{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
+
{| width="100%"
−
|+ 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]])
+
| style="vertical-align: top; width: 40%" |
−
|
+
{| class="jtable" style="float: left; width: 90%;"
−
{|style="background-color: transparent;" width="100%"
+
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|-
 
|-
−
|valign="top"|
+
! Official Release
−
{|style="background-color: transparent;" width="100%"
+
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
 
|-
 
|-
−
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
+
! 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
 
|-
 
|-
−
| style="padding: 3px 5px 10px 15px;"| ♦ Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].
+
! Official Release
 +
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
|-
 
|-
−
| 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!
+
! Python 3
−
|-
+
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
−
| 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!).
 
−
|}
 
−
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:refcard.png|155px]] Screenshot of the donated [[CheatSheet|PyMOL reference card]].
 
−
|}
 
 
|-
 
|-
−
|
+
! POSF
−
{|style="background-color: transparent;" width="100%"
+
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
|-
 
|-
−
|valign="top"|
+
! Tutorial
−
{|style="background-color: transparent;" width="100%"
+
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
−
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
+
! 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;"| &diams; PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
+
! 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;"| &diams; [[group]] command has been added.
+
! 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; The truly awesome [[grid_mode]] setting has been added.
+
! New Script
 +
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
|-
 
|-
−
| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
+
! Older News
 +
| See [[Older_News|Older News]].
 
|}
 
|}
−
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|125px]] Screenshot of [[grid_mode|Grid Mode]] in action.
+
|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="background-color: transparent;" width="100%"
+
|style="vertical-align: top; width: 18%"|
−
|-
+
<DynamicPageList>
−
|valign="top"|
+
imagecontainer=Covers
−
{|style="background-color: transparent;" width="100%"
+
randomcount=1
−
! 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!
 
−
|-
 
−
| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
 
−
|}
 
−
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:COLORAMA-screenshot.jpg|125px]] Screenshot of [[Colorama]].
 
−
|}
 
 
|}
 
|}

Latest revision as of 12:54, 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...

Extra fit

extra_fit aligns multiple objects to a reference object.

New in PyMOL 1.7.2

It can use any of PyMOL's pairwise alignment methods (align, super, cealign, fit...). More precisely it can use any function which takes arguments mobile and target, so it will for example also work with tmalign. Additional keyword arguments are passed to the used method, so you can for example adjust outlier cutoff or create an alignment object.

There are several similar commands/scripts for this job, like "A > align > all to this" from the PyMOL panel, the "alignto" command, align_all.py and super_all.py scripts from Robert Campbell.

Usage

extra_fit [ selection [, reference [, method ]]]

Example

This will align 4 structures on CA atoms using the super method. It will also create an alignment object.

<syntaxhighlight lang="python"> fetch 1e4y 1ake 4ake 3hpq, async=0 remove not chain A

extra_fit name CA, 1ake, super, object=aln_super </s ..→

A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=13571"