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Revision as of 18:34, 4 January 2016

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
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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...

CalcArea

=Overview=

This code will calculate the area of a given selection. If you have a bunch of disparate selections, or one selection made up of various objects then you can use this to find the area.

The Code

def calcArea(sel, ASA=0, density=3, quiet=1):
	"""
DESCRIPTION

    Calculate the area of an object or selection (as if it were one complete object).

ARGUMENTS

    sel = string: atom selection

    ASA = 0/1: solvent excluded or solvent accessible surface area

    density = int: sampling quality {default: 3}
	"""
	tName = "__temp__for__doArea__"
	cmd.create(tName, sel)
	cmd.flag("ignore", tName, "clear")
	cmd.set("dot_solvent", int(ASA), tName)
	cmd.set("dot_density", int(density), tName)
	theArea = cmd.get_area(tName)
	cmd.delete(tName)
	if not int(quiet):
		print 'Area (solvent %s): %.3f Angstroms^2' % (['excluded',
			'accessible'][int(ASA)], theArea)
	return theArea

cmd.extend('calcArea', calcArea)

See Also

A Random PyMOL-generated Cover. See Covers.