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== PyMol Wiki Home ==
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* updates on [http://pymol.sf.net PyMol]
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* a stable user-oriented documentation base
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* a thorough treatment of the PyMol program
| 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]]'''
* feature-rich scripts for general PyMol use
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==News==
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* Check out PyMol's new [[Cartoon#Nucleic_Acid_Representation|Nucleic Acid Rendering]]
| style="vertical-align: top; width: 40%" |
* Added [[DynoPlot]] script for plotting data within PyMol; an interactive Ramachandran plot.
{| class="jtable" style="float: left; width: 90%;"
* Added [[Kabsch]] script for optimal alignment of two sets of vectors.
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
* Some details have been released about [[0.99beta11]]'s release and new features.
|-
* A new map function is in the beta build, [[Map_Trim]].
! Official Release
* Details on how to build [[Peptide_Sequence| peptide sequences]] and [[Nucleic_Acid_Sequence| nucleic acid sequences]] by hand.
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
* New [[Transform_odb]] script to transform coordinates with .odb file from O or LSQMAN
|-
! New Plugin
| [[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
|-
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
! Selection keywords
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
! Plugin Update
| [[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
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! Older News
| See [[Older_News|Older News]].
|}
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See our [[Older_News]].
 
== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Latest revision as of 11:54, 12 March 2024

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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...

InterfaceResidues

The red residues were detected as being in the interface of the two proteins. This is PDB 1H4G from the Example below.

Overview

This script finds interface residues between two proteins or chains, using the following concept. First, we take the area of the complex. Then, we split the complex into two pieces, one for each chain. Next, we calculate the chain-only surface area. Lastly, we take the difference between the comeplex-based areas and the chain-only-based areas. If that value is greater than your supplied cutoff, then we call it an interface residue.

Usage

interfaceResidue complexName[, cA=firstChainName[, cB=secondChainName[, cutoff=dAsaCutoff[, selName=selectionNameToReturn ]]]]

where,

complexName

The name of the complex. cA and cB must be within in this complex

cA

The name of the first chain to investigate

cB

The name of the 2nd chain to investigate

cutoff

The dASA cutoff, in sqaure Angstroms

..→

A Random PyMOL-generated Cover. See Covers.


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