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Revision as of 09:57, 20 April 2016 by Speleo3 (talk | contribs) (PyMOL v1.8.2)
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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
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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...

Volume color

volume_color set or get the volume colors.

Usage

volume_color name [, ramp ]

Arguments

  • name = str: volume object name
  • ramp = str, list or empty: named ramp, space delimited string or list with (x, color, alpha, ...) or (x, r, g, b, alpha, ...) values. If empty, get the current volume colors.

Examples

Setting volume colors with one line:

fetch 1a00, map, type=2fofc, async=0
volume vol, map
volume_color vol, .8 cyan 0. 1. blue .3 2. yellow .3 

Using a named color ramp:

volume_ramp_new cyanblueyellow, \
    .8 cyan 0. \
    1. blue .3 \
    2. yellow .3
volume_color vol, cyanblueyellow

Getting the current volume ramp:

PyMOL>volume_color vol
### cut below here and paste into script ###
cmd.volume_ramp_new('ramp399', [\
     0.80, 0.00, 1.00, 1.00, 0.00, \
     1.00, 0.00, 0.00, 1.00, 0.30, \
     2.00, 1.00, 1.00, 0.00, 0.30, \
   ])
### cut above here and paste into script ###

See Also

A Random PyMOL-generated Cover. See Covers.