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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|+ 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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|-
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Select_sites
 
 
! New Script
 
! New Script
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| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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! New Script
 
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| [[b2transparency]] can set surface transparency based on atom b-factor
 
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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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! New Script
 
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| [[uniprot_features]] makes named selections for sequence annotations from uniprot
 
 
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! New Plugin
 
! New Plugin
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| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
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| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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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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! New Script
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! Official Release
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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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| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 
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! New Script
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! PyMOL Open-Source Fellowship
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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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| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 
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! New Script
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! Official Release
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| [[cyspka]] is an experimental surface cysteine pKa predictor.
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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
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| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
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| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 
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|-
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! New Script
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! New Plugin
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| [[spectrum_states]] colors states of multi-state object
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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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! New Plugin
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| [[TMalign]] is a wrapper for the TMalign program
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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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! Gallery Updates
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! 3D using Geforce
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| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
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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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|-
 
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! New Script
 
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| [[save_settings]] can dump all changed settings to a file
 
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! Tips & Tricks
 
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| Instructions for [[3d_pdf|generating 3D PDFs]] using 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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! 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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! 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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! 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.
 
 
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! Older News
 
! Older News
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|<div class="didyouknow" >
 
|<div class="didyouknow" >
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<DPL>
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<DynamicPageList>
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namespace=
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randomcount=1
 
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
 
escapelinks=false
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allowcachedresults=false
 
resultsheader=__NOTOC__ __NOEDITSECTION__
 
resultsheader=__NOTOC__ __NOEDITSECTION__
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randomcount=1
 
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mode=userformat
 
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addpagecounter=true
 
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
 
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
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|style="vertical-align: top; width: 18%"|
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<DynamicPageList>
 
imagecontainer=Covers
 
imagecontainer=Covers
 
randomcount=1
 
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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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</DPL>
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allowcachedresults=false
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</DynamicPageList>
  
 
|}
 
|}

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...

Clip

clip alters the near and far clipping planes

USAGE

clip {near|far|move|slab|atoms}, distance [,selection [,state ]]

EXAMPLES

clip near, -5           # moves near plane away from you by 5 A
clip far, 10            # moves far plane towards you by 10 A
clip move, -5           # moves the slab away from you by 5 A
clip slab, 20           # sets slab thickness to 20 A
clip slab, 10, resi 11  # clip 10 A slab about residue 11
clip atoms, 5, pept     # clip atoms in "pept" with a 5 A buffer
                        # about their current camera positions

PYMOL API

cmd.clip( string mode, float distance, string selection = None)

SEE ALSO
A Random PyMOL-generated Cover. See Covers.


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