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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|- 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="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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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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! 3D using Geforce
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! Official Release
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| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
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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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! New Software
 
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| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
 
 
|-
 
|-
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! New Script
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! Official Release
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| [[cgo_arrow]] draws an arrow between two picked atoms.
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
|-
 
|-
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! Tips & Tricks
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! Python 3
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
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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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| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
|-
 
|-
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! New Script
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! Tutorial
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| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
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| [[Plugins Tutorial]] updated for PyQt5
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|-
 
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! New Script
 
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| [[DistancesRH|Distances RH]]
 
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|-
 
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! PyMOL on the iPad
 
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| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.
 
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|-
 
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! OS X Compatibility
 
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| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
 
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|-
 
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! New Script
 
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| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
 
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|-
 
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! New Script
 
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| [[b2transparency]] can set surface transparency based on atom b-factor
 
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|-
 
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! New Extension
 
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| [[psico]] is a python module which extends PyMOL with many commands
 
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|-
 
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! New Script
 
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| [[uniprot_features]] makes named selections for sequence annotations from uniprot
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
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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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| [[set_phipsi]] can set phi/psi angles for all residues in a selection
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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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| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
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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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| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
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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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| [[cyspka]] is an experimental surface cysteine pKa predictor.
 
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|-
 
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! New Plugin
 
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| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].
 
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|-
 
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! New Script
 
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| [[spectrum_states]] colors states of multi-state object
 
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|-
 
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! New Script
 
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| [[TMalign]] is a wrapper for the TMalign program
 
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|-
 
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! Gallery Updates
 
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| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
 
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|-
 
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! New Script
 
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| [[save_settings]] can dump all changed settings to a file
 
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|-
 
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! Tips & Tricks
 
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| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
 
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|-
 
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! Wiki Update
 
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| Wiki has been updated. Please report any problems to the sysops.
 
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|-
 
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! New Scripts
 
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| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
 
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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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| [[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
 
! Older News
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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...

PyANM

Type PyMOL Plugin
Download plugins/pyanm.py
Author(s) Yuan Wang
License -
This code has been put under version control in the project Pymol-script-repo

Introduction

Elastic Network Models (ENM) have been successful in reproducing fluctuations for proteins of native conformations. ENM is a coarse-grained method for modeling protein dynamics, meaning in generally in ENM each residue is represented by one bead in its Alpha Carbon position. These beads are then connected by elastic springs if the distance between two beads fall under a cutoff value (usually within the range of 7 to 15 angstroms). For more details please read here.

PyANM is developed as a cross-platform Pymol Plugin to allow its users to build and visualize Anisotropic Network Models, a member of the ENM family. This plugin allows its users to draw arrows or make movies based on calculated mode motions, to draw all springs used to build the ANM within the protein, to color the protein based on its Mean Square Fluctuations ..→

A Random PyMOL-generated Cover. See Covers.


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