Center of mass

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Here is a script that calculates the center of mass from a selection. It gets hold of the coordinates with cmd.get_model. Make sure the atoms in the selection are of equal weight.

from pymol import cmd
from pymol.cgo import *

def centerOfMass(selection):
   ## assumes equal weights (best called with "and name ca" suffix)
   model = cmd.get_model(selection)
   for a in model.atom:
       x+= a.coord[0]
       y+= a.coord[1]
       z+= a.coord[2]
   return (x/len(model.atom), y/len(model.atom), z/len(model.atom))

cmd.load("/group/bioinf/Data/PDBLinks/1c7c.pdb")"domain", "/1c7c//A/143-283/ and name ca") ## selecting a domain


print "Center of mass: (%.1f,%.1f,%.1f)"% domainCenter"cartoon", "all")"spheres", "domain")

## Creating a sphere CGO
com = [COLOR, 1.0, 1.0, 1.0, SPHERE]+list(domainCenter) + [3.0] ## white sphere with 3A radius
cmd.load_cgo(com, "CoM")

cmd.zoom("1c7c", 1.0)"domain")

#ah@bioinfws19:~/Projects/PyMOL$ pymol -qc
#Center of mass: (-1.0,24.5,48.2)