[Chimera-users] radius of gyration
marek.maly at ujep.cz
Wed Feb 15 14:09:46 PST 2012
Isn't it radius of gyration (molecular) related rather to center of mass
of given molecule than to it's center of geometry ?
Dne Wed, 15 Feb 2012 21:05:24 +0100 Eric Pettersen <pett at cgl.ucsf.edu>
> 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:
> 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 Pettersen
> UCSF Computer Graphics Lab
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