# Difference between revisions of "Center of mass"

## Contents

### Description

This script calculates the true center-of-mass (COM) or the center-of-geometry (COG) for a given selection and returns the x, y, z values in the form of a Pseudoatom (rather than a CGO sphere). The benefit of using a Pseudoatom is that it can be selected and used in calculations. In addition, this script also iteratively goes through all states of a selection if more than one state exists and appends the corresponding COM/COG values as states into the Pseudoatom. The script itself is quite simple yet robust enough to be applied in different settings. As well, the calculation of the COM/COG is handled independently from the formation of the Pseudoatom and can be called as an independent function where applicable.

### Usage

```com selection [,state=None [,mass=None [,name=None]]]
```

### Examples

```fetch 1c3y, finish=1, multiplex=0

com 1c3y, state=1
#create a pseudoatom representing the 1c3y COG and store it as "1c3y_COM"

com 1c3y, state=1, name=COG
#create a pseudoatom representing the 1c3y COG and store it as "COG"

com 1c3y, state=1, name=COM, mass=1
#create a pseudoatom representing the 1c3y COM and store it as "COM"

com 1c3y, name=COM, mass=1
#create a single pseudoatom containing the COM for each state found in 1c3y and store it as "COM"
```

### PyMOL API

```from pymol import cmd

def com (selection,state=None,mass=None,name=None):

"""
Author: Sean Law
Michigan State University
slaw (at) msu . edu
"""
if (name == None):
name=selection+"_COM"
cmd.delete(name)

if (state != None):
x, y, z=get_com(selection,mass=mass)
print "%f %f %f" % (x, y, z)
cmd.pseudoatom(name,pos=[x, y, z])
cmd.show("spheres",name)
else:
for i in range(cmd.count_states()):
x, y, z=get_com(selection,mass=mass,state=i+1)
print "State %d:%f %f %f" % (i+1, x, y, z)
cmd.pseudoatom(name,pos=[x, y, z],state=i+1)
cmd.show("spheres",name)

return

cmd.extend("com",com)

def get_com (selection,state=1,mass=None):

"""
Author: Sean Law
Michigan State University
slaw (at) msu . edu
"""

atmass={'H':1.00800000000000, 'C':12.0110000000000, \
'N':14.0070000000000, 'O':15.9994000000000, \
'P':30.9740000000000, 'S':32.0600000000000, \
'F':18.9980000000000
}

totmass=0.0
if (mass!=None):
print "Calculating mass-weighted COM"

state=int(state)
model = cmd.get_model(selection,state)
x,y,z=0,0,0
for a in model.atom:
if (mass != None):
if (a.name in atmass):
x+= a.coord*atmass[a.name]
y+= a.coord*atmass[a.name]
z+= a.coord*atmass[a.name]
totmass+=atmass[a.name]
else:
return
else:
x+= a.coord
y+= a.coord
z+= a.coord

if (mass!=None):
return x/totmass, y/totmass, z/totmass
else:
return x/len(model.atom), y/len(model.atom), z/len(model.atom)
cmd.extend("get_com", get_com)
```

### Previous Implementation

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

For a sample application, see: "Convergent Evolution Examples"

```## Author: Andreas Henschel 2006

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)
x,y,z=0,0,0
for a in model.atom:
x+= a.coord
y+= a.coord
z+= a.coord
return (x/len(model.atom), y/len(model.atom), z/len(model.atom))

cmd.select("domain", "/1c7c//A/143-283/ and name ca") ## selecting a domain

domainCenter=centerOfMass("domain")

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

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