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! Official Release
 
! Official Release
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| [http://pymol.org PyMOL v1.8.6 has been released] on March 9, 2017.
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
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! Official Release
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! Python 3
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| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
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! New Script
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! POSF
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
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! New Plugin
 
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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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! Official Release
 
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| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
 
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! PyMOL Open-Source Fellowship
 
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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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! Official Release
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! Tutorial
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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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| [[Plugins Tutorial]] updated for PyQt5
 
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! New Plugin
 
! New Plugin
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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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| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
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! New Plugin
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! Selection keywords
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
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! New Plugin
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! Plugin Update
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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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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
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! 3D using Geforce
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! New Script
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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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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
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! Older News
 
! Older News

Latest revision as of 03:21, 22 June 2021

hosted by SBGridlogo2.jpg
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News See Older News.
Did you know...

Cluster Count

= Overview =

This script calculates statistics on the B-values for all atoms in the selected object, prints the information on screen and appends it to a file called "cluster_count.txt".


Usage

cluster_count object


Example

cluster_count 1ubq

#output on screen:

Number of atoms in ' 1ubq ':  602
Minimum and Maximum B-values:  2.0 42.75
Average B-value:  13.4131063029
Standard deviation of the B-values:  8.70767140923
This data will be appended to cluster_count.txt

#output in file cluster_count.txt; the format is:
#objectname N minB maxB aveB stdevB
1ubq            602    2.000   42.750   13.413    8.708


The Code

<source lang="python">

  1. Script: cluster_count.py
  2. Copyleft 2010 Martin Christen

from pymol import cmd,stored def cluster_count(selection): 

       """
AUTHOR

Martin Christen

DESCRIPTION

This script calculates statistics on the B-values for all atoms in
the selected object, prints the information on screen and appends
it to the  ..→
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://wiki.pymol.org/index.php?title=Main_Page&oldid=14896"