Difference between revisions of "Main Page"

Type	Python Module
Download	poseview.py
Author(s)	Thomas Holder
License	BSD-2-Clause
	This code has been put under version control in the project Pymol-script-repo

Latest revision as of 03:21, 22 June 2021

hosted by

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...

PoseView

poseview is a PyMOL wrapper for the PoseView program. PoseView generates 2D structure-diagrams of protein-ligand complexes.

Setup

You need the poseview executable and a valid license file. Example for a launcher script which should be saved to /usr/bin/poseview so that PyMOL can find it:

#!/bin/sh
POSEVIEW_PATH="/opt/poseview-1.1.2-Linux-x64"
export BIOSOLVE_LICENSE_FILE="$POSEVIEW_PATH/poseview.lic"
exec "$POSEVIEW_PATH/poseview" "$@"

Usage

poseview [ ligand [, protein [, width [, height [, filename [, exe [, state ]]]]]]]

Example

fetch 1a00, async=0
poseview chain C and resn HEM

A Random PyMOL-generated Cover. See Covers.

@@ Line 1: / Line 1: @@
-<br>
+__NOTOC__
-* [[TOPTOC|'''Table of Contents''']]
+{| 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;"
+|}
-* [[Special:Allpages|Alphabetized Index of all pages]]
+{| 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]]'''
+|}
-* [[Improvements|Discussion of PyMolWiki Improvements]]
+{| width="100%"
-<br>
+| 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 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 fellows announced for 2018-2019]
+|-
+! 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
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+|}
+|
+|style="vertical-align: top; width: 18%"|
+<DynamicPageList>
+imagecontainer=Covers
+randomcount=1
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+listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
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-== PyMol Wiki Home ==
+|}
-You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.
-We provide
-* updates on [http://pymol.sf.net PyMol]
-* a stable user-oriented documentation base
-* a thorough treatment of the PyMol program
-* feature-rich scripts for general PyMol use
-== New Users ==
-Welcome!  New users who wish to contribute appropriate content are welcome to join.  Feel free to add any appropriate content; make an account and get started!
-==News==
-===PyMol===
-* Pymol 1.0 is out!
-* [http://delsci.info/dsc/ PyMol Official Documentation] is also available for subscribers.
-===Plugins/Scripts===
-* [[EMovie]] plugin added.  Easy movies in PyMol using a GUI.
-* [[DYNMAP]] plugin page created.  Check it out!
-* [[Cealign|CE Align v0.8-RBS]] released.  Better than before.  See test case comparisons.
-* [[Slerpy]], a set of pymol command extensions to simplify complex movie making is now available.
-* Updated the [[Kabsch#The_New_Code|Kabsch]] code with a more elegant solution; fixed a small rotation bug.
-===News Archive===
-*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!)
-* [[Settings|PyMol Settings]]  (6 newly documented; only 470 to go...)
-* [[:Special:Allpages| All Pages]]
-* [[:Category:Plugins|Plugins]]
-* [[:Special:Categories| See All Categories]]