[Chimera-users] radius of gyration

[Marek Maly]

Hello,

Isn't it radius of gyration (molecular) related rather to center of mass  
(gravity)
of given molecule than to it's center of geometry ?

    Best wishes,

         Marek




Dne Wed, 15 Feb 2012 21:05:24 +0100 Eric Pettersen <pett at cgl.ucsf.edu>  
napsal/-a:

> 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
>
>
>
>
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