Difference between revisions of "Main Page"

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__NOTOC__
 
__NOTOC__
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{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"
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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;"
 
{| align="center" style="padding-bottom: 3em;"
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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: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:bold; color: #6d6003; font-size: 140%; font-family: serif;"
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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.
−
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-family: serif;"
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|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
 
| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
 
| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
−
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; 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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|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
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|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; border-bottom: 1px solid #fff;" |Quick Links
 
|-  
 
|-  
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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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|-
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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]]'')
 
||'''[[PyMOL_mailing_list|Getting Help]]'''
 
||'''[[PyMOL_mailing_list|Getting Help]]'''
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|-
 
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! Official Release
 
! Official Release
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| [http://pymol.org PyMOL v1.8.2 has been released] on April 20, 2016.
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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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! POSF
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| [https://pymol.org/fellowship PyMOL Open-Source Fellowship program] accepting applications for 2018-2019
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|-
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! New Plugin
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| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
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|-
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! Selection keywords
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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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|-
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! Plugin Update
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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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! New Plugin
 
! New Plugin
 
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 
| [[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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! Official Release
 
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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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! Official Release
 
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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

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...

Radius of gyration

Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.querying#gyradius

This script does calcualate the radius of gyration of a molecule.

Thanks to Tsjerk Wassenaar for posting this script on the pymol-users mailing list!

The function was added to psico as "gyradius".

<source lang="python"> from pymol import cmd import math

def rgyrate(selection='(all)', quiet=1):

DESCRIPTION 

   Radius of gyration

USAGE 

   rgyrate [ selection ]
   
   try:
       from itertools import izip
   except ImportError:
       izip = zip
   quiet = int(quiet)
   model = cmd.get_model(selection).atom
   x = [i.coord for i in model]
   mass = [i.get_mass() for i in model]
   xm = [(m*i,m*j,m*k) for (i,j,k),m in izip(x,mass)]
   tmass = sum(mass)
   rr = sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in izip(x,xm))
   mm = sum((sum(i)/tmass)**2 for i in izip(*xm))
   rg = math.sqrt(rr/tmass - mm)
   if not quiet:
        ..→
A Random PyMOL-generated Cover. See Covers.


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