Difference between revisions of "Main Page"

Type	Python Module
Download	get_colors.py
Author(s)	Andreas Warnecke
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...

Get colors

get_colors contains two functions that can be useful when working with colors
- get_colors : returns all available PyMOL colors
- get_random_color : returns a random available PyMOL color

Note that basic colors can be accessed manually without this script from the PyMOL menu under Setting --> Colors...
For instruction on setting up plugin import see Git intro or Plugin Manager

Usage

get_colors [ selection [, quiet ]]
get_random_color [ selection [, quiet ]]

Examples

..→

A Random PyMOL-generated Cover. See Covers.

@@ Line 1: / Line 1: @@
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-|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | 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: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
+|}
+{| 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:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
+|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
-| New accounts: email jason (dot) vertrees (@) gmail dot com
+| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
-|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
+|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
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+{| 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; color #61021F; 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:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
 |-
-| style="font-size: 1.1em; color #61021F; 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;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
 |-
-| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
+| 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]]'')
-||'''[[GoogleSearch]]'''
+||'''[[PyMOL_mailing_list|Getting Help]]'''
 |}
@@ Line 25: / Line 29: @@
 |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
 |-
-! New Script
+! Official Release
-| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure.
+| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
-A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
+|-
+! Python 3
+| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 |-
-! New Script
+! POSF
-| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript.
+| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
-Like web Jmol, but MUCH faster. Try it out!
 |-
-! New Script
+! Tutorial
-| [[cyspka]] is an experimental surface cysteine pKa predictor.
+| [[Plugins Tutorial]] updated for PyQt5
 |-
 ! New Plugin
-| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
+| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
-|-
-! New Script
-| [[spectrum_states]] colors states of multi-state object
-|-
-! New Script
-| [[TMalign]] is a wrapper for the TMalign program
-|-
-! Gallery Updates
-| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
-|-
-! New Script
-| [[save_settings]] can dump all changed settings to a file
-|-
-! Tips & Tricks
-| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
-|-
-! Wiki Update
-| Wiki has been updated. Please report any problems to the sysops.
 |-
-! New Scripts
+! Selection keywords
-| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
+| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 |-
-! New Script
+! Plugin Update
-| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
+| [[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
-| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]].
+| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
-|-
-! New Script
-| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
 |-
 ! Older News
@@ Line 77: / Line 61: @@
 |-
 |<div class="didyouknow" >
-<DPL>
+<DynamicPageList>
-namespace=
+randomcount=1
 category=Commands|Plugins|Script_Library|Settings
 includepage=*
-includemaxlength=450
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-randomcount=1
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-addpagecounter=true
 listseparators=,<h3>[[%PAGE%]]</h3>,,\n
-</DPL>
+</DynamicPageList>
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@@ Line 94: / Line 76: @@
 |
 |style="vertical-align: top; width: 18%"|
-<DPL>
+<DynamicPageList>
 imagecontainer=Covers
 randomcount=1
@@ Line 101: / Line 83: @@
 listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 ordermethod=none
-</DPL>
+allowcachedresults=false
+</DynamicPageList>
 |}

Difference between revisions of "Main Page"

Latest revision as of 03:21, 22 June 2021

Get colors

Usage

Examples

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