Main Page

From PyMOLWiki
Revision as of 23:16, 2 January 2016 by Inchoate (talk | contribs)
Jump to navigation Jump to search
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...

Surface carve selection

Animation with a moving pseudoatom as the surface_carve_selection

With the surface_carve_selection and surface_carve_cutoff settings, the visibility of a molecular surface can be limited to the proximity of an atom selection.

Unlike when showing surface representation only for a subset of atoms, the visibility is controlled on the vertex (surface point) level, not the atom level.

The value of surface_carve_selection must be a named selection (created with select), it cannot be a selection expression (e.g. "chain A" won't work).

Example

Visibility control on the vertex level. Hide surface points which are more than 5 Angstrom away from carvesele:

fetch 1rx1, async=0
as cartoon
select carvesele, organic
set surface_carve_selection, carvesele
set surface_carve_cutoff, 5
show surface
show sticks, carvesele

Compare to visibility control on the atom level. Hide surface for atoms which are more ..→

A Random PyMOL-generated Cover. See Covers.