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News & Updates
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released on December 3, 2014.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
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 v1.7.2 have all been released on August 4, 2014.
Official Release PyMOL, AxPyMOL, and JyMOL v1.7 have all been released today, January 14, 2014.
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.
New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News See Older News.
Did you know...

Pucker

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

DESCRIPTION

pucker.py is a PyMol script that returns the sugar pucker information (phase, amplitude, pucker) for a given selection.

This script uses its own dihedral calculation scheme rather than the get_dihedral command. Thus, it is lightning fast!

If a selection does not contain any ribose sugars then an error message is returned.

USAGE

load the script using the run command

pucker selection
#Calculates the sugar information for the given selection
 
pucker selection, state=1
#Calculates the sugar information for the given selection in state 1
 
pucker selection, state=0 
#Iterates over all states and calculates the sugar information for the given selection

EXAMPLES

#fetch 1BNA.pdb
fetch 1bna
 
#Select DNA only
#Otherwise, you will get an error for water not having sugars
select DNA, not solvent
 
#Execute pucker  [[Pucker|..→]]
A Random PyMOL-generated Cover. See Covers.


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