Hi :)
The radius of gyration is not that tough. Here's a python script to do
it in pymol. Do note that the hydrodynamic radius is something
related, but different.
from pymol import cmd
import math
def rgyrate(selection):
# Get the atoms for the selection
model=cmd.get_model(selection).atom
# Extract the coordinates
x=[i.coord for i in model]
# Get the masses
mass=[i.get_mass() for i in model]
# Mass-weighted coordinates
xm=[(m*i,m*j,m*k) for (i,j,k),m in zip(x,mass)]
# Sum of masses
tmass=sum(mass)
# First part of the sum under the sqrt
rr=sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in zip(x,xm))
# Second part of the sum under the sqrt
mm=sum((sum(i)/tmass)**2 for i in zip(*xm))
# Radius of gyration
rg=math.sqrt(rr/tmass-mm)
# Print it...
print "Radius of gyration:", rg
return rg
cmd.extend("rgyrate",rgyrate)
Hope it helps,
Tsjerk
On Thu, Mar 31, 2011 at 3:03 PM, Julio Cesar da Silva
<julio.si...@lnbio.org.br> wrote:
> Dear Kanika,
>
>
>
> I do not know how to calculate the Rg using PyMOL. If it is possible, I
> would also like to know how. However, there are other possibilities.
>
> Do you have the pdb file of the molecule from what you want to calculate the
> radius of gyration? If so, you may use the program CRYSOL (download:
> http://www.embl-hamburg.de/biosaxs/crysol.html), which is used for
> comparison with SAXS data. When you run that program, you can search within
> the log file the parameter “Envelope Rg”. But, keep in mind that the program
> takes into account a solvation layer of about 3 Angstroms.
>
> You can also try the HydroPro program
> (http://leonardo.inf.um.es/macromol/programs/hydropro/hydropro.htm), which I
> believe that makes the Rg calculation, but I rarely use this program for
> that. I am sure that HydroPro can provide you the hydrodynamic radius, but I
> am not sure about the Rg.
>
>
>
> Regards,
>
> Julio
>
>
>
> De: kanika sharma [mailto:ksharma...@gmail.com]
> Enviada em: quinta-feira, 31 de março de 2011 14:46
> Para: pymol-users
> Assunto: [PyMOL] radius of gyration
>
>
>
> After going through the script library and tutorial, I couldn't find
> information about calculating the radius of gyration. Is this possible in
> pymol? And after this I want to generate a virtual cube around it of a
> specific length.
>
>
>
> Thanks,
>
> Kanika
>
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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