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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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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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!
 +
|- 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:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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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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|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
 
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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 Software
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! Official Release
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| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
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| [https://pymol.org PyMOL v2.2 has been released] on July 24, 2018.
 
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|-
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! New Script
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! POSF
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| [[cgo_arrow]] draws an arrow between two picked atoms.
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| [https://pymol.org/fellowship PyMOL Open-Source Fellowship program] accepting applications for 2018-2019
 
|-
 
|-
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! Tips & Tricks
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! New Plugin
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
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| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
 
|-
 
|-
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! New Script
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! Selection keywords
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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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| 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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| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
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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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| [[DistancesRH|Distances RH]]
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
|-
 
|-
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! PyMOL on the iPad
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! New Plugin
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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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| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 
|-
 
|-
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! OS X Compatibility
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! New Plugin
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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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| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
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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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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
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|-
 
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! New Script
 
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| [[set_phipsi]] can set phi/psi angles for all residues in a selection
 
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|-
 
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! New Script
 
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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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|-
 
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! 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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|-
 
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! New Script
 
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| [[cyspka]] is an experimental surface cysteine pKa predictor.
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].
+
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
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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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! New Script
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! 3D using Geforce
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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]].
+
| 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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! 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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Revision as of 04:49, 24 July 2018

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 v2.2 has been released on July 24, 2018.
POSF PyMOL Open-Source Fellowship program accepting applications for 2018-2019
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
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
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be 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.
Older News See Older News.
Did you know...

Assembly

When loading mmCIF structure files, the assembly setting controls whether PyMOL loads the asymmetric unit (assembly="") or a biological unit (e.g. assembly="1"). Assembly identifiers in mmCIF files can be arbitrary strings, but usually are numeric and most files define at least assembly "1".

New in PyMOL 1.8

Assemblies with more than one symmetry copy are loaded as multi-state objects with all_states=on. The assemblies should be equivalent to the pdb1 files which are available from the PDB ftp server.

Examples

Download the ASU and the first assembly, show them side by side. 

set assembly, ""
fetch 3bw1, asu, async=0

set assembly, 1
fetch 3bw1, assembly1, async=0

set grid_mode

See Also
A Random PyMOL-generated Cover. See Covers.


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