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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! 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.
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| [http://pymol.org PyMOL v1.8.2 has been released] on April 20, 2016.
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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
 
 
|-
 
|-
 
! New Script
 
! New Script
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| [[b2transparency]] can set surface transparency based on atom b-factor
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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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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| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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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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! 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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! 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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! 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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|-
 
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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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| [[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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! New Script
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! 3D using Geforce
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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]].
+
| 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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| [[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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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 10:57, 20 April 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
Official Release PyMOL v1.8.2 has been released on April 20, 2016.
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...

Normalize ccp4 maps

Good default? It has been suggested to change the default of this setting to off. If you agree or disagree, please leave a comment on the discussion page.

The normalize_ccp4_maps settings (default: on) controls whether or not PyMOL normalizes the data from a ccp4 map file upon loading. The data is shifted and scaled so that mean=0.0 and stdev=1.0.

Normalization is done on the raw data array, not across the unit cell. This means that if the raw data doesn't exactly cover an integral number of asymmetric units, the result will be different than for example when loading the same file into Coot, which normalizes across the cell.

Normalization should be turned off before loading, in cases like:

  • the map file has already been normalized, for example with CCP4’s mapmask program
  • you want to specify mesh contour levels in raw units (e/A^3) instead of rmsd (sigma). This is recommended if you want to make figures that match the display in Coot.

Usage

<source lang="python">

  1. load map and normalize data

set normalize_ccp4_maps, on load somemap.ccp4

  1. load map as-is (without normalization)

set normalize_ccp4_maps, off load ..→

A Random PyMOL-generated Cover. See Covers.


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