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)
 
(554 intermediate revisions by 50 users not shown)
Line 1: Line 1:
−
== PyMol Wiki Home ==
+
__NOTOC__
−
You have reached the (new) 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/]]
 +
|}
 +
{| 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;"
 +
|}
  
−
== [[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]]
+
|+ 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
−
* [[Command Language]]
+
|-
−
* [[Atom Selections]]
+
| 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]]'''
−
* [[Ray-tracing]]
+
|-
−
* [[Movies and Animations]]
+
| 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]]'''
−
* [[Cartoon Representations]]
+
|-
−
* [[Settings Reference (all settings and what they do)]]
+
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
−
* [[Stereo 3D Display]]
+
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
−
** [[Hardware Options]]
+
||'''[[PyMOL_mailing_list|Getting Help]]'''
−
** [[Linux XFree86 Configuration]]
+
|}
−
* [[Crystallography Aplications]]
 
−
** [[Symmetry]]
 
−
** [[Electron Density]]
 
−
* [[Arbitrary Graphics Objects]]
 
−
* [[Python Integration]]
 
−
* [[Scenes]]
 
  
−
== [[User Additions]] ==
+
{| width="100%"
−
* [[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)
+
! Official Release
−
** [[List of Plugins]]
+
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
−
** [[Tutorial on writing plugins]]
+
|-
−
** [[Others]]
+
! Python 3
−
----
+
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
−
* [[Structure Alignment]] (Nat Echols)
+
|-
−
** [[Structure Alignment Editor]]
+
! POSF
−
* [[3rd Party Applications]]
+
| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
−
** [[Movies]]
+
|-
−
** [[Codecs]]
+
! 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>
  
−
----
+
|}
−
~--
 
−
----
 

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...

Fetch Path

Fetch_Path sets the default path that PyMOL uses to load files from before it tries to download them from the PDB.

Details

If you have a local copy of the PDB on your machine, say in directory /spc/pdb then, once you set Fetch_Path to that directory the fetch command will look in /spc/pdb before going to the PDB for your file. Also, the files fetched from the PDB are stored here once downloaded. PyMOL will only look for files starting with the pdb code in lower case.

Examples

On Linux or MacOS: 

set fetch_path, /spc/pdb

On Windows: 

set fetch_path, D:\mypdbs

Using ~/fetch_path: 

cmd.set('fetch_path', cmd.exp_path('~/fetch_path'), quiet=0)

Hints

Put this in your pymolrc to make it permanent.

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


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