[Chimera-users] radius of gyration

[Eric Pettersen]

On Feb 14, 2012, at 6:07 PM, Daniel Gurnon wrote:

> Hi Eric,
> The radius of gyration interest stems from a little project I'm  
> starting with an undergrad. I'm interested in the radius of gyration  
> because I'm curious about how accurate our pictures of biomolecules  
> are, at least the ones that come from crystal structures. I'd like  
> to compare predictions of size-related behavior derived from the pdb  
> with measurements of size in solution, using gel filtration, SAXS,  
> or light scattering. That said, I don't know if I want center of  
> geometry or principal axis!  Any advice?

Hi Dan,
	I'm no expert, but it sounds like you want the radius of gyration  
from the center of geometry.  Nonetheless, I'm cc'ing this to the  
chimera-users in case any others have thoughts.
	In an old posting to chimera-users, Elaine Meng provided a Fortran  
program to compute the radius of gyration:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003648.html

I've attached a Python script that will print the center of geometry  
and radius of gyration from that center in Chimera's reply log.  Run  
the script simply by opening it with File->Open.  Depending on whether  
you feel nearby waters and ions will contribute to the measurements  
you are trying to model, you may or may not want to delete water and  
ions before running the script.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120215/b5d9f650/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: radius-of-gyration.py
Type: text/x-python-script
Size: 357 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120215/b5d9f650/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120215/b5d9f650/attachment-0001.html>