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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!
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|+ 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/]]
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{| align="center" style="padding-bottom: 3em;"
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|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
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|- 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.
 
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
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|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
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| New accounts: email jason (dot) vertrees (@) gmail dot com
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| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
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| 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]]'''
 
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| 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]]'''
 
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
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||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
 
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
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! New Plugin
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! Official Release
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| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
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! Python 3
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| [[spectrum_states]] colors states of multi-state object
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
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! New Script
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! POSF
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| [[TMalign]] is a wrapper for the TMalign program
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
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! Tutorial
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| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
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| [[Plugins Tutorial]] updated for PyQt5
 
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! New Script
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! New Plugin
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| [[save_settings]] can dump all changed settings to a file
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| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
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! Tips & Tricks
 
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| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
 
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| Wiki has been updated. Please report any problems to the sysops.
 
 
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! New Scripts
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! Selection keywords
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| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
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! New Script
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! Plugin Update
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| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. 
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
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! New Script
 
! New Script
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| [[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]].
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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! New Script
 
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| [[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.
 
 
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! Older News
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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...

Rotkit

Type Python Script
Download rotkit.py
Author(s) Troels E. Linnet
License BSD
This code has been put under version control in the project Pymol-script-repo

Introduction

This script-kit is a collection of small script to be able to precisely to put a molecule (like a dye) where you want in relation to a protein.

You can also create rotational states of a domain or simulate a dye freedom.

It simply makes the PyMOL TTT matrixes, in a easy and user friendly way. The calls to the functions available in PyMOL, takes care of all the conversion of input and such.

If you are interested in this, you might also want to check out the PyMOL Chempy module that is included in PyMOL. It provides handy vector and matrix functions.

Functions available in PyMOL

  • rotateline(Pos1,Pos2,degangle,molecule):
    "Pos1->Pos2" define a line whereabout "molecule" will be rotated "degangle" degrees
    rotateline Pos1=P513C_CA, Pos2=P513C_CB, degangle=5, molecule=Atto590
    rotateline Pos1=dyeatom87, Pos2=dyeatom85, degangle=10, ..→
A Random PyMOL-generated Cover. See Covers.


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