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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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{| 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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|
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|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-family: serif; font-style: italic;"
 
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| For Educational downloads go to http://pymol.org/educational
 
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| Due to large amounts of spam, we've halted unsupervised account creation.  Please contact jason . vertrees (@) gmail dot com to get a new account.
 
 
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{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
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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;"
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|-  
 
|-  
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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; color #61021F; 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; 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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| 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]]'')
 
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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||'''[[GoogleSearch]]'''
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||'''[[PyMOL_mailing_list|Getting Help]]'''
 
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|-
 
|-
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! New Scripts
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! Official Release
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| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
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|-
 
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! New Script
 
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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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|-
 
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! 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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|-
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! New Script
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! Python 3
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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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| 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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| [[PluginDirectory]]: How to set up a personal plugin directory
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
|-
 
|-
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! New Script
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! Tutorial
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| Add focal blur to images [[FocalBlur]].
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| [[Plugins Tutorial]] updated for PyQt5
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|-
 
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! New Script
 
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| Visualize VDW clashes with [[show bumps]]
 
 
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! New Plugin
 
! New Plugin
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| Color by [[DSSP]] or [[Stride]] secondary structure assignment
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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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! New Script
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! Selection keywords
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| There is a new script to calculate the [[Radius of gyration]]
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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 Command
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! Plugin Update
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| [[Map_set]] Performs a given operation on a map: can create consensus volumes, for example.
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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
 
|-
 
|-
 
! New Script
 
! New Script
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| [[ColorByDisplacement]] Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins.
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
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|-
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! New Script
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! Older News
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| [[DisplacementMap]] Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.
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| See [[Older_News|Older News]].
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|-
 
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! New Script
 
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| Two new scripts: [[AAindex]] and [[Sidechaincenters]]
 
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! New Plugin
 
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| [[CAVER_2.0]] update to the CAVER plugin.
 
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! New Script
 
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| [[AngleBetweenHelices]] calculates the angle between two helices.
 
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|-
 
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! Search
 
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| [[GoogleSearch]] widget fixed.
 
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! New Script
 
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| [[Spectrumany]] creates color gradients with arbitrary color sequences.
 
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! New Script
 
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| [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
 
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! New Script
 
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| [[Center Of Mass]] has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere). 
 
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! New Script
 
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| [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
 
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! New Scripts
 
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| [[ResDe]] is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.
 
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! New Script
 
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| See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.
 
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! New Script
 
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| See [[Supercell]], the new script for making XxYxZ supercells.
 
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|-
 
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! New Script
 
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| See [[Split_Object_Along_Axis]], for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.
 
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|-
 
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! New Script
 
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| See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.
 
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|-
 
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! Server updates
 
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| The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend.  We are now fully functional.  A '''deep''' thanks to [http://www.bitgnome.net BitGnome] for donating time and hardware for the PyMOL project.
 
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|-
 
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! fetch_host setting
 
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| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
 
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! Fetch
 
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| [[Fetch]] has been updated to also load electron density maps.
 
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|-
 
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! Schrodinger Buys PyMOL
 
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| Schrodinger has purchased PyMOL.  Development, support and open-source fun to continue!  Read about the [http://www.schrodinger.com/news/47/ sale].
 
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|-
 
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! User Movie
 
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| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL. 
 
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|-
 
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! New setting
 
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| [[surface_cavity_mode]] to change how PyMOL displays cavities.
 
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|-
 
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! Search fixed.
 
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| Thanks to a eagle-eyed user, our search has been fixed.  Please let us know if you have any search-related problems.
 
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! New Command
 
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| [[Cache]]—stores information on structures, so we don't have to recompute them.
 
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! Warren
 
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| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
 
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! Setting
 
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| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
 
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! New Script
 
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| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
 
 
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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...

Get Color Indices

get_color_indices in combination with get_color_tuple will retrieve the RGB values for colors. 
print cmd.get_color_indices()

will retrieve the Pymol color names and corresponding internal color indices. The Pymol names can be used to designate color for objects, see Color. To retrieve a single index for a specific color name, use get_color_index instead. 

print cmd.get_color_tuple(index-number)
will retrieve individual RGB components when index-number is replaced with one of the color indices from above.

The color index, an integer, gets returned when color is returned while employing Iterate. You can thus use the get_color_tuple command above to convert that to RGB color values if you need to use the colors outside Pymol.

Tangentially related is the fact you can name additional colors, 

set_color color-name, [r,b,g]

will create a new color that will appear in the GUI list. From the open-source ..→

A Random PyMOL-generated Cover. See Covers.


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