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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{| 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!
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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.
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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="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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||'''[[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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! PyMOL Open-Source Fellowship
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! Official Release
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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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| [https://pymol.org PyMOL v2.4 has been released] on May 20, 2020.
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
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! Official Release
 
! Official Release
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014.
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| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
 
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! Official Release
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! POSF
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014.
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
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! New Plugin
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! Tutorial
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
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| [[Plugins Tutorial]] updated for PyQt5
 
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! New Plugin
 
! New Plugin
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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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| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
 
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|-
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! 3D using Geforce
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! Selection keywords
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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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| 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 Plugin
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! Plugin Update
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
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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
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! 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
 
! New Script
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| [[cgo_arrow]] draws an arrow between two picked atoms.
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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! Tips & Tricks
 
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
 
 
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! Older News
 
! Older News
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Revision as of 04:38, 20 May 2020

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 v2.4 has been released on May 20, 2020.
Python 3 New Python 3 compatibility guide for scripts and plugins
Official Release PyMOL v2.3 has been released on February 11, 2019.
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
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
Older News See Older News.
Did you know...

Propka

Type Python Script
Download propka.py
Author(s) Troels E. Linnet
License BSD
This code has been put under version control in the project Pymol-script-repo

Acknowledgement

propka.py contact and relies on the result from the propka server

The PROPKA method is developed by the Jensen Research Group , Department of Chemistry, University of Copenhagen.

Introduction

This script can fetch the pka values for a protein from the propka server. The "propka" function downloads the results and processes them.
It also automatically writes a pymol command file and let pymol execute it. This command file make pka atoms, rename them, label them and color them according to the pka value.

If you put the mechanize folder and the propka.py script somewhere in your pymol search path, then getting the pka values is made super easy. By the way, did you know, that you don't have to prepare the .pdb file by adding/removing hydrogens? The ..→

A Random PyMOL-generated Cover. See Covers.


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