Difference between revisions of "Main Page"

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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 Plugin
 +
| [[Bondpack]] is a 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
 
| [[Bondpack]] is a a collection of PyMOL plugins for easy visualization of atomic bonds.
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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! Tips & Tricks
 
! Tips & Tricks
 
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
 
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
|-
 
! New Script
 
| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
 
|-
 
! New Script
 
| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
 
|-
 
! New Script
 
| [[DistancesRH|Distances RH]]
 
|-
 
! PyMOL on the iPad
 
| 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.
 
|-
 
! OS X Compatibility
 
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
 
|-
 
! New Script
 
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
 
|-
 
! New Script
 
| [[b2transparency]] can set surface transparency based on atom b-factor
 
|-
 
! New Extension
 
| [[psico]] is a python module which extends PyMOL with many commands
 
|-
 
! New Script
 
| [[uniprot_features]] makes named selections for sequence annotations from uniprot
 
|-
 
! New Plugin
 
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
 
|-
 
! New Script
 
| [[set_phipsi]] can set phi/psi angles for all residues in a selection
 
|-
 
! New Script
 
| [[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.
 
|-
 
! New Script
 
| [[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!
 
|-
 
! New Script
 
| [[cyspka]] is an experimental surface cysteine pKa predictor.
 
|-
 
! New Plugin
 
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].
 
|-
 
! New Script
 
| [[spectrum_states]] colors states of multi-state object
 
|-
 
! New Script
 
| [[TMalign]] is a wrapper for the TMalign program
 
|-
 
! Gallery Updates
 
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
 
|-
 
! New Script
 
| [[save_settings]] can dump all changed settings to a file
 
|-
 
! Tips & Tricks
 
| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
 
|-
 
! Wiki Update
 
| Wiki has been updated. Please report any problems to the sysops.
 
|-
 
! New Scripts
 
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
 
|-
 
! New Script
 
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. 
 
|-
 
! New Script
 
| [[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]].
 
|-
 
! New Script
 
| [[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

Revision as of 12:45, 18 November 2013

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
New Plugin Bondpack is a 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:


A Random PyMOL-generated Cover. See Covers.