This is a read-only mirror of pymolwiki.org

Difference between revisions of "Main Page"

From PyMOL Wiki
Jump to navigation Jump to search
m (2 revisions)
 
(205 intermediate revisions by 18 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%"
 
−
| ''The community-run support site for the [http://pymol.org PyMOL] molecular viewer.''
 
−
|-
 
 
|}
 
|}
−
{| align="center" style="width:90%; margin-bottom: 20px"
+
{| 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!
−
{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
+
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
−
! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
+
| 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;"
−
| 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]]!
+
| 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="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
+
{| 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
−
| [[TOPTOC|'''Table of Contents''']]
+
|-  
−
|| [[Special:Allpages|Index of all pages]]
+
| 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]]'''
−
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
 
−
|-
 
−
| [[:Category:Tutorials|Tutorials]] <font color='red'><b>!</b></font>
 
−
|| [[:Category:Commands|Commands]]
 
−
|| '''Settings''': [[Settings|All]]  | [[:Category:Settings|Documented]]
 
 
|-
 
|-
−
| [[:Category:Script_Library|'''Script Library''']] <font color='red'><b>!</b></font>
+
| 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]]'''
−
|| [[:Category:Plugins|'''Plugins''']]
 
−
|| [[:Special:Categories| See All Categories]]
 
−
|-
 
−
| [[:Category:FAQ|Frequently Asked Questions]]
 
−
|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
 
−
|| [[About| '''About PyMOL''']]
 
−
|-
 
−
| ''Track:'' [http://sourceforge.net/tracker/?atid=104546&group_id=4546&func=browse Bugs] [http://sourceforge.net/tracker/?group_id=4546&atid=354546 Feature Req] [http://sourceforge.net/tracker/?group_id=4546&atid=204546 Support Req]
 
 
|-
 
|-
 +
| 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]]'''
 
|}
 
|}
−
|- style="color: #333; font-weight:bold; font-size: 20px; text-align:center; padding: 10em;"
+
 
−
|  
+
{| width="100%"
−
<!--
+
| style="vertical-align: top; width: 40%" |
−
[http://www.pymol.org/ PyMOL 1.2] has been released! -->
+
{| 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
−
|}
 
−
{| 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]])
 
−
|
 
−
{|style="background-color: transparent;" width="100%"
 
 
|-
 
|-
−
|valign="top"|
+
! Official Release
−
{|style="background-color: transparent;" width="100%"
+
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
|-
 
|-
−
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
+
! Python 3
 +
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
|-
 
|-
−
| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL is known to work under Mac OS X 10.6 (Snow Leopard) using the new Fink.  See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
+
! POSF
 +
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
|-
 
|-
−
| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
+
! Tutorial
 +
| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[Space]]&mdash; new command to control PyMOL's usage of color spaces.
+
! New Plugin
 +
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
|-
 
|-
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[CGOCylinder]]&mdash; information on CGO cylinders and circles in PyMOL.
+
! 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: 2px 5px 0px 15px;"| &diams; '''[http://www.pymol.org/ PyMOL] 1.2 is out!
+
! 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: 2px 5px 0px 15px;"| &diams; Check out the artist who integrates PyMOL into [http://winkleman.com/artist/seriesview/1406/376 his work].
+
! New Script
 +
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
|-
 
|-
−
| style="padding: 2px 5px 0px 15px;"| &diams; If you use the sequence viewer alot, or have lots of openGL text on the screen, try boosting your performance with [[Texture_fonts]].
+
! 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...
 
|-
 
|-
−
| style="padding: 2px 5px 0px 15px;"| &diams; '''PyMOL now integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
+
|<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>
 
|}
 
|}
−
|valign="middle" width="150px" style="padding: 0 20px 20px 0" |[[Image:080602cnen.pdf.jpg|125px]] Another cover made with PyMOL.  See [[Covers]].
 
−
|}
 
−
|-
 
 
|
 
|
−
{|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, Plugins &amp; Tutorials
+
escapelinks=false
−
|-
+
openreferences=true
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[Spectrumbar]]&mdash; powerful new script for making custom spectrum bars in PyMOL.
+
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
−
|-
+
ordermethod=none
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[CollapseSel]]&mdash; simple script to compress selection lists: eg. instead of i. 1+2+3+4+5 you get 1-5.
+
allowcachedresults=false
−
|-
+
</DynamicPageList>
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[SuperSym]]&mdash; incredible script for handling crystallographic symmetry operations.
+
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[CgoCircle]]&mdash; draw CGO circles in PyMOL; surround objects or selections with circles.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[MovieSchool]] &mdash; PyMOL Wiki's Movie School.  Learn how to make movies in PyMOL!
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[alphaToAll]] &mdash; Expands your desired alpha-carbon property down to all atoms in the residue.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[interfaceResidues]] &mdash; Finds interface residues in a complex.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSurfaceResidues]] &mdash; Find and show (if you want) surface exposed resiues in PyMOL.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[ToGroup]] &mdash; Converts a multistate object into a group of single state objects.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSeq]] &mdash; Find sequence or regular expression of amino acids in a protein.
 
−
|-
 
−
| style="padding: 2px 5px 10px 15px;"| &diams; [[Modevectors]] &mdash; creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[Pucker]] &mdash; finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
 
−
|}
 
−
|valign="middle" width="150px" style="padding: 0 20px 20px 0" |[[Image:Sb_default.png|165px]] Example image from the new script, [[Spectrumbar]].
 
−
|}
 
−
{|style="background-color: transparent;" width="100%"
 
−
|-
 
−
|valign="top"|
 
−
{|style="background-color: transparent;" width="100%"
 
−
|-
 
−
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; [[Label]]s page was thoroughly refurbished.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance.  The downtime was <10 minutes.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; '''Please note the "Go" and "Search" buttons in the search bar.  They're not the same, and entering text and hitting ENTER is the same as using the "Go" button.'''  Please try using the "Search" button; we're using a new search engine and it has cool new features.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; Documented a few more settings.  Also, check out the cool, [[Huge_surfaces]] page for handling very large objects and representing them as surfaces, in PyMOL.
 
−
|-
 
−
| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
 
−
|}
 
−
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:Science090410.jpg|125px]] Sample Cover from the [[Covers]] gallery.
 
−
|}
 
 
|}
 
|}

Latest revision as of 03:21, 22 June 2021

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 v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
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 use ter records

When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of TER record is inserted wherever the residue id is not sequential. To suppress this feature, set pdb_use_ter_records value to 0 before saving protein molecules.

Version History

  • 2.3.0 new implementation, works correctly with gaps
  • 1.8.4 feature removed
  • <= 1.8.2 feature broken for various use cases (e.g. gaps)
  • <= 1.5.0.4 feature broken for HETATM polymer residues (e.g. MSE)

Example

get pdb_use_ter_records  # return current value of pdb_use_ter_records
set pdb_use_ter_records, 0

PyMOL API

cmd.set('pdb_use_ter_records', 0)

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


Retrieved from "http://wiki.pymol.org/index.php?title=Main_Page&oldid=14896"