Difference between revisions of "Main Page"

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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 on the iPad
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! Official Release
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| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.
+
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014.
 
|-
 
|-
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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, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014.
 
|-
 
|-
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! New Script
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! New Plugin
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| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
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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
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
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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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|-
 
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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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| [[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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|-
 
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! New Script
 
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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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! New Script
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! 3D using Geforce
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| [[cyspka]] is an experimental surface cysteine pKa predictor.
+
| 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
 
! New Plugin
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| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
 
|-
 
|-
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! New Script
+
! New Software
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| [[spectrum_states]] colors states of multi-state object
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| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
 
|-
 
|-
 
! New Script
 
! New Script
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| [[TMalign]] is a wrapper for the TMalign program
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| [[cgo_arrow]] draws an arrow between two picked atoms.
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|-
 
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! Gallery Updates
 
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| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
 
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|-
 
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! New Script
 
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| [[save_settings]] can dump all changed settings to a file
 
 
|-
 
|-
 
! Tips & Tricks
 
! Tips & Tricks
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| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from 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.
 
 
|-
 
|-
 
! Older News
 
! Older News
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category=Commands|Plugins|Script_Library|Settings
 
category=Commands|Plugins|Script_Library|Settings
 
includepage=*
 
includepage=*
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includemaxlength=450
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includemaxlength=1050
 
escapelinks=false
 
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resultsheader=__NOTOC__ __NOEDITSECTION__
 
resultsheader=__NOTOC__ __NOEDITSECTION__

Revision as of 09:57, 8 August 2014

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) GoogleSearch
News & Updates
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released on August 4, 2014.
Official Release PyMOL, AxPyMOL, and JyMOL v1.7 have all been released today, January 14, 2014.
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.
New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News See Older News.
Did you know...

The DPL extension (version 2.3.0) produced a SQL statement which lead to a Database error.
The reason may be an internal error of DPL or an error which you made,
especially when using DPL options like titleregexp.
Query text is:
SELECT DISTINCT `pmw_page`.page_namespace AS page_namespace,`pmw_page`.page_title AS page_title,`pmw_page`.page_id AS page_id, `pmw_page`.page_title AS sortkey, `pmw_page`.page_counter AS page_counter FROM `pmw_page` INNER JOIN `pmw_categorylinks` AS cl0 ON `pmw_page`.page_id=cl0.cl_from AND (cl0.cl_to='Commands' OR cl0.cl_to='Plugins' OR cl0.cl_to='Script_Library' OR cl0.cl_to='Settings') WHERE 1=1 AND `pmw_page`.page_namespace IN (0) AND `pmw_page`.page_is_redirect=0 ORDER BY page_title ASC LIMIT 500 OFFSET 0

Error message is:
Unknown column 'pmw_page.page_counter' in 'field list' (localhost)


A Random PyMOL-generated Cover. See Covers.


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