This is a read-only mirror of pymolwiki.org

Difference between revisions of "Radius of gyration"

From PyMOL Wiki
Jump to navigation Jump to search
(example)
m
Line 40: Line 40:
 
[[File:Radius_of_gyration_Example.png|300px|thumb|right]]
 
[[File:Radius_of_gyration_Example.png|300px|thumb|right]]
  
This example used the radius of gyration and the [[Center_Of_Mass|center of mass]] to display a semitransparent sphere.
+
This example uses the radius of gyration and the [[Center_Of_Mass|center of mass]] to display a semitransparent sphere.
  
 
<source lang="python">
 
<source lang="python">
 
from pymol import cmd, stored, util
 
from pymol import cmd, stored, util
import centerOfMass, rgyrate
+
import centerOfMass, radiusOfGyration
  
 
cmd.set('sphere_transparency', 0.5)
 
cmd.set('sphere_transparency', 0.5)
Line 52: Line 52:
 
cmd.show('cartoon', 'chain A')
 
cmd.show('cartoon', 'chain A')
  
stored.gyradius = rgyrate.rgyrate('chain A and polymer')
+
stored.gyradius = radiusOfGyration.rgyrate('chain A and polymer')
 
centerOfMass.com('chain A and polymer', object='com')
 
centerOfMass.com('chain A and polymer', object='com')
 
cmd.alter('last com', 'vdw=stored.gyradius')
 
cmd.alter('last com', 'vdw=stored.gyradius')

Revision as of 18:58, 31 March 2011

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

Radius of gyration Example.png

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')

stored.gyradius = radiusOfGyration.rgyrate('chain A and polymer')
centerOfMass.com('chain A and polymer', object='com')
cmd.alter('last com', 'vdw=stored.gyradius')

util.cbc()

See Also

Center Of Mass, COM