Radius of gyration
From PyMOLWiki
This script does calcualate the radius of gyration of a molecule.
Thanks to Tsjerk Wassenaar for posting this script on the pymol-users mailing list!
from pymol import cmd from itertools import izip import math def rgyrate(selection='(all)', quiet=1): ''' DESCRIPTION Radius of gyration USAGE rgyrate [ selection ] ''' quiet = int(quiet) model = cmd.get_model(selection).atom x = [i.coord for i in model] mass = [i.get_mass() for i in model] xm = [(m*i,m*j,m*k) for (i,j,k),m in izip(x,mass)] tmass = sum(mass) rr = sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in izip(x,xm)) mm = sum((sum(i)/tmass)**2 for i in izip(*xm)) rg = math.sqrt(rr/tmass - mm) if not quiet: print "Radius of gyration: %.2f" % (rg) return rg cmd.extend("rgyrate", rgyrate) # vi:expandtab
Example
This example uses the radius of gyration and the center of mass to display a semitransparent sphere.
from pymol import cmd, stored, util import centerOfMass, radiusOfGyration cmd.set('sphere_transparency', 0.5) cmd.fetch('2xwu') cmd.hide('everything') cmd.show('cartoon', 'chain A') r = radiusOfGyration.rgyrate('chain A and polymer') centerOfMass.com('chain A and polymer', object='com', vdw=r) util.cbc()
