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Revision as of 22:16, 2 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 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...

Zoom

zoom scales and translates the window and the origin to cover the atom selection.

USAGE

zoom [ selection [,buffer [, state [, complete ]]]]

EXAMPLES

# auto zoom depending on what's loaded in PyMOL
zoom

#
zoom complete=1

# zoom on just chain A
zoom (chain A)

# zoom on residue 142
zoom 142/

# zoom consistenly 20 Ang from each object at the center
center prot1
zoom center, 20

# prot1 and prot2 will have the same exact zoom factor
center prot2
zoom center, 20

PYMOL API

 
cmd.zoom( string selection, float buffer=0.0,
          int state=0, int complete=0 )

NOTES

state = 0 (default) use all coordinate states
state = -1 use only coordinates for the current state
state > 0  use coordinates for a specific state

complete = 0 or 1:

Normally the zoom command tries to guess an optimal zoom level for visualization, balancing closeness against occasional clipping of atoms out of the field of view. You can change this behavior by setting ..→

A Random PyMOL-generated Cover. See Covers.


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