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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{| class="jtable" style="float: left; width: 90%;"
 
{| class="jtable" style="float: left; width: 90%;"
 
|+ 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
 +
|-
 +
! New Script
 +
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 +
|-
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! New Plugin
 +
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 
|-
 
|-
 
! Official Release
 
! Official Release
−
| [[http://pymol.org|PyMOL, AxPyMOL, and JyMO v1.7 have all been released]] today, January 14, 2014.
+
| [http://pymol.org 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
 +
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 +
|-
 +
! New Plugin
 +
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 
|-
 
|-
 
! 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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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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! 3D using Geforce
 
! 3D using Geforce
 
| 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.
 
| 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.
−
|-
 
−
! New Plugin
 
−
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
 
−
|-
 
−
! 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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| [[cgo_arrow]] draws an arrow between two picked atoms.
 
−
|-
 
−
! Tips & Tricks
 
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
 
 
|-
 
|-
 
! Older News
 
! Older News
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|-
 
|-
 
|<div class="didyouknow" >
 
|<div class="didyouknow" >
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<DynamicPageList>
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category=Commands|Plugins|Script_Library|Settings
 
category=Commands|Plugins|Script_Library|Settings
 
includepage=*
 
includepage=*
 
includemaxlength=1050
 
includemaxlength=1050
 
escapelinks=false
 
escapelinks=false
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resultsheader=__NOTOC__ __NOEDITSECTION__
 
resultsheader=__NOTOC__ __NOEDITSECTION__
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listseparators=,<h3>[[%PAGE%]]</h3>,,\n
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
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|style="vertical-align: top; width: 18%"|
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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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|}
 
|}

Revision as of 11:52, 26 January 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
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...

RotationAxis

Type Python Script
Download draw_rotation_axis.py
Author(s) Pablo Guardado Calvo
License
This code has been put under version control in the project Pymol-script-repo

This script will draw a CGO cylinder representing a rotation axis for a given transformation. It's very useful for drawing the axes of rotational symmetry in an oligomeric assembly.

The idea is to align two molecules/domains/chains/selections (using cmd.super) and extract the trasformation (TTT) matrix (T). The direction of the rotation axis, and a point are obtained from T and are used to create a cgo object representing the axis. The script generates two measures: one in the graphical screen (the rotation axis value, and the norm of the translation vector along the rotation axis) and some basic information in the command-line (the transformation matrix, the rotation angle, distance between centroids, and some pml lines that you can use to reproduce the axis...)

As always with these type of things, you have to use it at your own risk. I did not try all possible combinations, but if you find a ..→

A Random PyMOL-generated Cover. See Covers.


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