Difference between revisions of "Main Page"

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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
 
| style="font-size: 1.1em; color #61021F; 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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! OS X Compatibility
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! Official Release
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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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| [http://pymol.org PyMOL v1.8.2 has been released] on April 20, 2016.
 
|-
 
|-
 
! New Script
 
! New Script
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| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
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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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| [[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
 
 
|-
 
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! New Plugin
 
! New Plugin
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| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
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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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|-
 
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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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! Official Release
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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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| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 
|-
 
|-
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! New Script
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! PyMOL Open-Source Fellowship
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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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| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 
|-
 
|-
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! New Script
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! Official Release
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| [[cyspka]] is an experimental surface cysteine pKa predictor.
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
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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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! New Script
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! New Plugin
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| [[spectrum_states]] colors states of multi-state object
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 
|-
 
|-
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! New Script
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! New Plugin
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| [[TMalign]] is a wrapper for the TMalign program
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| [[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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! Gallery Updates
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! 3D using Geforce
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| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
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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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|-
 
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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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|<div class="didyouknow" >
 
|<div class="didyouknow" >
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<DPL>
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<DynamicPageList>
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namespace=
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randomcount=1
 
category=Commands|Plugins|Script_Library|Settings
 
category=Commands|Plugins|Script_Library|Settings
 
includepage=*
 
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includemaxlength=450
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includemaxlength=1050
 
escapelinks=false
 
escapelinks=false
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resultsheader=__NOTOC__ __NOEDITSECTION__
 
resultsheader=__NOTOC__ __NOEDITSECTION__
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randomcount=1
 
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mode=userformat
 
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addpagecounter=true
 
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
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|style="vertical-align: top; width: 18%"|
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<DynamicPageList>
 
imagecontainer=Covers
 
imagecontainer=Covers
 
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 
ordermethod=none
 
ordermethod=none
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</DPL>
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allowcachedresults=false
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</DynamicPageList>
  
 
|}
 
|}

Revision as of 10:57, 20 April 2016

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v1.8.2 has been released on April 20, 2016.
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.
Official Release PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
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...

Caver2

Type PyMOL Plugin
Download plugins/Caver2_1_2.py
Author(s) CAVER 2.0
License -
This code has been put under version control in the project Pymol-script-repo

CAVER 2.0 is a software tool for protein analysis leading to detection of channels. Channels are in fact void pathways leading from buried cavities to the outside solvent of a protein structure. Studying of these pathways is highly important in the area of drug design and molecular enzymology.

Ukazky-plugin.png

CAVER 2.0 provides rapid, accurate and fully automated calculation of channels not only for static molecules, but also for dynamic molecular simulations.
CAVER 2.0 facilitates analysis of any molecular structure including proteins, nucleic acids or inorganic materials.

Ukazky.png

CAVER 2.0 can be used in two possible ways. If you are accustomed with the PyMOL ..→

A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=12352"