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||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
||'''[[PyMOL_mailing_list|Getting Help]]'''
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Revision as of 03:29, 21 October 2015

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
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...

LatticeGenerator

This is a simple script to generate a repeating atom lattice. It just writes atoms in PDB format, and PyMOL will automatically connect adjacent atoms when loading the PDB file. You may adjust the c and/or x_shift, y_shift arrays to obtain different geometries, and the number of iterations in the loops to adjust the lattice size.

See also the thread on pymol-users mailing list.

<syntaxhighlight lang="python"> from numpy import array

  1. coordinates of the repeating unit (from cyclohexane)

c = array([[ 0.064, 2.851, -1.085 ],

          [ 0.260,   1.969,   0.159 ]])

x_shift = array([ 1.67441517, -0.91605961, 1.66504574]) y_shift = array([-0.69477826, -0.40578592, 2.40198410])

  1. template string for PDB hetatom line

s = 'HETATM %4d C03 UNK 1 %8.3f%8.3f%8.3f 0.00 0.00 C '

out = open('lattice.pdb', 'w')

i = 0 for x in range(10):

   for y in range(10):
       for v in (c +  ..→
A Random PyMOL-generated Cover. See Covers.