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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! Official Release
 
! Official Release
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| [[PyMOL, AxPyMOL, and JyMO v1.7 have all been released|http://pymol.org]] today, January 14, 2014.
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| [http://pymol.org PyMOL v1.8.2 has been released] on April 20, 2016.
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|-
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! New Script
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
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! New Plugin
 
! New Plugin
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| [[Bondpack]] is a a collection of PyMOL plugins for easy visualization of atomic bonds.
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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 Plugin
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! Official Release
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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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| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
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|-
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! PyMOL Open-Source Fellowship
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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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|-
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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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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
|-
 
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! New Plugin
 
! New Plugin
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
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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 Software
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! New Plugin
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| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
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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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| [[cgo_arrow]] draws an arrow between two picked atoms.
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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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! Tips & Tricks
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! 3D using Geforce
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
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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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! Older News
 
! Older News
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
 
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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...

Split Object Along Axis

== Overview ==

I have a number of small molecules that I am looking at. Many of these small molecules have distinct sections which are connected by a single bond. In a separate program I am writing, I would like to rotate each section around the given bond. I wanted a script that would allow me 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. If there is a 2nd bond which connects the 2 sections of atoms, the script will still run and terminate, but the two selections won't make much sense!

To use, just call splitObjAlongAxis(axisSelection, outFileName) where: axisSelection is a selection that includes 2 atoms. These atoms define the axis which we are splitting across. outFileName is an optional file name where the script will spit three lines. The first line will be the two atom id's of the axis. The second line will be a list of atom id's in the selection generated, and the third line ..→

A Random PyMOL-generated Cover. See Covers.


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