Difference between revisions of "Main Page"

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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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|
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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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| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
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|  
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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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|- style="text-align:center; font-weight:bold; color: #333; font-size: 140%; font-family: serif;"
 
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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: #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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|-
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! New Script
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! Official Release
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| Add focal blur to images [[http://www.pymolwiki.org/index.php/FocalBlur]].
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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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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| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
 
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|-
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! New Script
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! Official Release
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| There is a new script to calculate the [[Radius of gyration]]
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
|-
 
|-
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! New Command
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! Python 3
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| [[Map_set]] Performs a given operation on a map: can create consensus volumes, for example.
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
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|-
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! New Script
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! POSF
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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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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
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|-
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! New Script
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! Tutorial
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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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| [[Plugins Tutorial]] updated for PyQt5
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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
 
! New Plugin
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| [[CAVER_2.0]] update to the CAVER plugin.
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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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| [[AngleBetweenHelices]] calculates the angle between two helices.
 
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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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! Selection keywords
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| [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
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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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|-
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! New Script
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! Plugin Update
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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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| [[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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| [[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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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
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|-
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! New Scripts
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! Older News
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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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| See [[Older_News|Older News]].
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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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! 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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! 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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! New setting
 
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| [[surface_cavity_mode]] to change how PyMOL displays cavities.
 
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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 12:54, 12 March 2024

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 v3.0 has been released on March 12, 2024.
New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
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 fellowship announced for 2022-2023
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...

SuperSym

Type PyMOL Plugin
Download plugins/SuperSymPlugin.py
Author(s) Stuart Ballard
License
This code has been put under version control in the project Pymol-script-repo
Symmetry partners for 1hpv showing 6-1 screw axis
Full cell of symmetry partners with symmetry axes displayed

SuperSym is a PyMOL plugin providing a large number of tools for visualization of space groups; unit cells; and symmetry axes, operators, and partners.

The original source code is available from https://sourceforge.net/projects/supersym/

Dependencies

PyMOL, cctbx and numpy must all be compiled with the same Python distribution! See CCTBX.

This plugin was developed in 2010 for PyMOL version 1.2r1 and has not been updated since.

Bugs

Symmetry axes are not defined for all space groups, and do not display properly for some.

Acknowledgments

Primary coding and development was done by Stuart Ballard. All comments, questions, and issues ..→

A Random PyMOL-generated Cover. See Covers.


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