Difference between revisions of "Main Page"

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(added information about the new plugin MOLE for PyMOL)
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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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! New Plugin
+
! New Script
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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.
+
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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|-
 
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! 3D using Geforce
 
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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.
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
+
| [[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 Software
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! Official Release
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| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
+
| [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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| [[cgo_arrow]] draws an arrow between two picked atoms.
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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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! Tips & Tricks
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! Official Release
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
+
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
|-
 
|-
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! New Script
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! New Plugin
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| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
+
| [[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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| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
 
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|-
 
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! New Script
 
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| [[DistancesRH|Distances RH]]
 
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|-
 
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! PyMOL on the iPad
 
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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.
 
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|-
 
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! OS X Compatibility
 
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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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|-
 
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! New Script
 
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| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
 
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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.
+
| [[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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| [[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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|-
 
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! New Script
 
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| [[cyspka]] is an experimental surface cysteine pKa predictor.
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
−
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].
+
| [[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.
 
|-
 
|-
−
! New Script
+
! 3D using Geforce
−
| [[spectrum_states]] colors states of multi-state object
+
| 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 Script
 
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| [[TMalign]] is a wrapper for the TMalign program
 
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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
 
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|-
 
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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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|-
 
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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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|<div class="didyouknow" >
 
|<div class="didyouknow" >
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resultsheader=__NOTOC__ __NOEDITSECTION__
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imagecontainer=Covers
 
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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...

BiologicalUnit

Note: PyMOL 1.8 can load biological units from mmCIF files with the assembly setting.

This script can be used to re-create biological units for proteins. (This was created as a workaround of PyMOL's semi-functioning Symexp command.) It's also a fun script to play with for learning about symmetry.

  • single unit, before running this program

  • after the expansion of the 60 units

  • Example creating the biological unit for PDB 1RMV created from fiber diffraction.

Usage

load /path/to/some/pdbFile.pdb
symMat = readSymmetry("/path/to/some/pdbFile.pdb","pdbFile")
biologicalUnit("mates", "pdbFile", symMat)

The Code

<source lang="python">

  2. Jason Vertrees <Jason-dot-Vertrees-at-schrodinger_dot_com>, 2010.

import pymol from pymol import cmd

def readSymmetry(inFile, verbose=None): 

  ..→
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=12276"