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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||'''[[PyMOL_mailing_list|Getting Help]]'''
 
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! New Script
 
! New Script
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| [[spectrum_states]] colors states of multi-state object
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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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! New Plugin
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| [[TMalign]] is a wrapper for the TMalign program
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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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! 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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! New Script
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! Official Release
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| [[save_settings]] can dump all changed settings to a file
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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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! Tips & Tricks
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! PyMOL Open-Source Fellowship
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| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
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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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! Wiki Update
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! Official Release
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| Wiki has been updated. Please report any problems to the sysops.
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
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|-
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! New Scripts
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! New Plugin
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| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
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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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| [[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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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 
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! New Script
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! New Plugin
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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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| [[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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! New Script
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! 3D using Geforce
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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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| 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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! Older News
 
! Older News
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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
 
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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...

Spectrumbar

Type Python Script
Download spectrumbar.py
Author(s) Sean M. Law
License -
This code has been put under version control in the project Pymol-script-repo

Description

Often times one may color their structure based upon some predefined color spectrum. However, this alone is not helpful when dealing with publication images. The purpose of this script is to allow the user to draw their own custom spectrum bar to accompany their structural images.

Further work will be done to improve the functionality of this script. Please feel free to contact the author for function requests.

USAGE

load the script using the run command 

spectrumbar (RGB_Colors,radius=1.0,name=spectrumbar,head=(0.0,0.0,0.0),tail=(10.0,0.0,0.0),length=10.0, ends=square)

Please see the script comments for further custom options. Once the script completes, it will generate a new object called "spectrumbar" (which can be changed through the options) which is a cylinder colored according to the user-specified colors.

Note: It is strongly ..→

A Random PyMOL-generated Cover. See Covers.


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