Re: [ccp4bb] Principal axes and moment of inertia matrix

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CCP4bb <-- 2008 <-- January 2008 <-- 10 January 2008

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Subject: Re: Principal axes and moment of inertia matrix
From: "Ralf W {- dot -} Grosse-Kunstleve" rwgk {- at -} YAHOO {- dot -} COM
Date: 2008-01-10

Hi Buz,

> Does anyone have a python routine that can be used to calculate the
> moment of inertia matrix and principal axes of a selection of atoms?

If you have Phenix, CCI Apps or just cctbx installed, try the script below.
Example:

mmtbx.python script.py 1NSF.pdb 'resname GLU and resid 735'

See also: http://www.phenix-online.org/download/

Ralf

from mmtbx.monomer_library import pdb_interpretation
from mmtbx.monomer_library import server
from scitbx.math import principal_axes_of_inertia
from scitbx.array_family import flex
from libtbx.utils import Usage, plural_s
import sys, os

def run(args):
if (len(args) < 2 or not os.path.isfile(args[0])):
raise Usage('pdb_file "atom_selection" [...]')
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=args[0],
log=sys.stdout)
print
acp = processed_pdb_file.all_chain_proxies
selection_cache = acp.stage_1.selection_cache()
aal = acp.stage_1.atom_attributes_list
for selection_string in args[1:]:
print selection_string
isel = acp.iselection(string=selection_string, cache=selection_cache)
print " %d atom%s selected" % plural_s(isel.size())
points = flex.vec3_double()
for i_seq in isel:
print " %s" % aal[i_seq].pdb_format()
points.append(aal[i_seq].coordinates)
pai = principal_axes_of_inertia(points=points)
print " center of mass:", pai.center_of_mass()
print " inertia tensor:", pai.inertia_tensor()
es = pai.eigensystem()
print " eigenvalues:", list(es.values())
print " eigenvectors:", list(es.vectors())
print

if (__name__ == "__main__"):
run(sys.argv[1:])

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 10 January 2008

Previous message:
Subject: Re: crystallization robot
From: David Briggs drdavidcbriggs {- at -} GMAIL {- dot -} COM
Date: 2008-01-10

Next message:
Subject: Two postdoc positions at SGX Pharmaceuticals
From: Shane Atwell satwell {- at -} SGXPHARMA {- dot -} COM
Date: 2008-01-10