[Chimera-users] calculating radius of gyration

[Elaine Meng]

> On Dec 14, 2021, at 11:10 AM, Simon.Chapman <simon.chapman at open.ac.uk> wrote:
> 
> Hello again Elaine. All going very well with Chimera, and I've introduced the software to some more of mt students.
> 
> But, is there a way to plot radius of gyration from the simualtion data? I would have thought somehow the RMSD over time should allow that?
> 
> Best wishes

Hi Simon,
Thanks for introducing others to Chimera!  

I'm not the expert on this topic, so I had to consult with others to answer this question.  Just as a reminder, it's recommended to send questions to chimera-users at cgl.ucsf.edu (CC'd here) unless what you are sending needs to remain private.  I don't know everything (surprise!) or I might not understand your question as well as somebody else does.

RMSD compares different sets of coordinates, so I don't think that gets you anything like the radius of gyration of a single set of coordinates.

There are some scripts to calculate radius of gyration on the Chimera Python Scripts page:
<https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco