Hi Filippo,
Here is a python script that calculates the Center of mass for a given
selection
and creates a CGO sphere there. It is is not 100% exact as it only
weighs C-Alpha atoms.
This is exactly how pymol centers selections: when you run the script,
the domain is centered and if you rotate the structure with the mouse,
the CGO will remain centered.
I hope that helps.
Best,
Andreas
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[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")
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
cmd.load_cgo(com, "CoM")
cmd.zoom("1c7c", 1.0)
cmd.center("domain")
#...@bioinfws19:~/Projects/PyMOL$ pymol -qc centerOfMass4.py
#Center of mass: (-1.0,24.5,48.2)
#...@bioinfws19:~/Projects/PyMOL$
Filippo Marchioni wrote:
Hi all!
Two questions:
Does anyone know how to read the coordinates (x,y,z) of a selected atom
in a protein?
Or even better
Does anyone know how to visualize the center of mass of the protein,
reset the axis (x,y,z) using the centroid as origin and then calculate
the distance of a resi or an atom from the new origin?
Thanks!
best
Filo
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Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany
Phone: +49 351 463 40063
EMail: a...@biotec.tu-dresden.de
