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{| 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: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;"
|+ 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.
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
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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;"
 
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
{| 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]]'')
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
||'''[[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
|-
|-
! New Script
! Official Release
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. 
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
! 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]].
|-
! 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.
|-
! New Script
| [[PluginDirectory]]: How to set up a personal plugin directory
|-
! New Script
| Add focal blur to images [[FocalBlur]].
|-
! New Script
| Visualize VDW clashes with [[show bumps]]
|-
|-
! New Plugin
! New Plugin
| Color by [[DSSP]] or [[Stride]] secondary structure assignment
| [[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
|-
! New Script
| There is a new script to calculate the [[Radius of gyration]]
|-
|-
! New Command
! Official Release
| [[Map_set]] Performs a given operation on a map: can create consensus volumes, for example.
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
! New Script
! Python 3
| [[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.
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
! New Script
! POSF
| [[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.
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
! New Script
! Tutorial
| Two new scripts: [[AAindex]] and [[Sidechaincenters]]
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
! New Plugin
! New Plugin
| [[CAVER_2.0]] update to the CAVER plugin.
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
! New Script
| [[AngleBetweenHelices]] calculates the angle between two helices.
|-
|-
! Search
! Selection keywords
| [[GoogleSearch]] widget fixed.
| 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
| [[Spectrumany]] creates color gradients with arbitrary color sequences.
| [[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
| [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
! New Script
! Older News
| [[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). 
| See [[Older_News|Older News]].
|-
! New Script
| [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
|-
! New Scripts
| [[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.
|-
! New Script
| See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.
|-
! New Script
| See [[Supercell]], the new script for making XxYxZ supercells.
|-
! New Script
| 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.
|-
! New Script
| See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.
|-
! Server updates
| 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.
|-
! fetch_host setting
| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
|-
! Fetch
| [[Fetch]] has been updated to also load electron density maps.
|-
! Schrodinger Buys PyMOL
| Schrodinger has purchased PyMOL.  Development, support and open-source fun to continue!  Read about the [http://www.schrodinger.com/news/47/ sale].
|-
! User Movie
| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL. 
|-
! New setting
| [[surface_cavity_mode]] to change how PyMOL displays cavities.
|-
! Search fixed.
| Thanks to a eagle-eyed user, our search has been fixed.  Please let us know if you have any search-related problems.
|-
! New Command
| [[Cache]]—stores information on structures, so we don't have to recompute them.
|-
! Warren
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
|-
! Setting
| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
|-
! New Script
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
|}
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Latest revision as of 11:54, 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...

Extra fit

extra_fit aligns multiple objects to a reference object.

New in PyMOL 1.7.2

It can use any of PyMOL's pairwise alignment methods (align, super, cealign, fit...). More precisely it can use any function which takes arguments mobile and target, so it will for example also work with tmalign. Additional keyword arguments are passed to the used method, so you can for example adjust outlier cutoff or create an alignment object.

There are several similar commands/scripts for this job, like "A > align > all to this" from the PyMOL panel, the "alignto" command, align_all.py and super_all.py scripts from Robert Campbell.

Usage

extra_fit [ selection [, reference [, method ]]]

Example

This will align 4 structures on CA atoms using the super method. It will also create an alignment object.

<syntaxhighlight lang="python"> fetch 1e4y 1ake 4ake 3hpq, async=0 remove not chain A

extra_fit name CA, 1ake, super, object=aln_super </ ..→

A Random PyMOL-generated Cover. See Covers.


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