Re: [ccp4bb] Radius of Gyration

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Detergent Crystals In Tube?
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From: Poul Nissen pn {- at -} MB {- dot -} AU {- dot -} DK
Date: 2008-10-31

Subject: Re: Radius of Gyration
From: Konrad Hinsen hinsen {- at -} CNRS-ORLEANS {- dot -} FR
Date: 2008-10-31

On 30.10.2008, at 04:39, David M Shechner wrote:

> I was wondering if anyone knew of a quick method (say, a publicly-
> available
> script, or subroutine in a CCP4 program) by which one might
> calculate the
> Radius of Gyration of a molecule, given its pdb file. Any ideas?

The Python script below will calculate the radius of gyration for the
assembly of all molecules specified in a PDB file (typically the
asymmetric unit). To run it, you need the Molecular Modelling
Toolkit, available from

http://dirac.cnrs-orleans.fr/MMTK/

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen@cnrs-orleans.fr
---------------------------------------------------------------------

from MMTK import *
from MMTK.PDB import PDBConfiguration
from MMTK.PDBMoleculeFactory import PDBMoleculeFactory
from Scientific import N

conf = PDBConfiguration('some_molecules.pdb')
factory = PDBMoleculeFactory(conf)
molecules = Collection(factory.retrieveMolecules())

def radiusOfGyration(m):
natoms = m.numberOfAtoms()
center = sum((atom.position() for atom in m.atomList()),
Vector(0., 0., 0.)) / natoms
sum_r = sum(((atom.position()-center).length()**2
for atom in m.atomList()))
return N.sqrt(sum_r/natoms)

print radiusOfGyration(molecules)/Units.Ang, "Angstrom"

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Detergent Crystals In Tube?
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2008-10-30

Next message:
Subject: Re: Detergent Crystals In Tube?
From: Poul Nissen pn {- at -} MB {- dot -} AU {- dot -} DK
Date: 2008-10-31