On Dec 14, 2021, at 11:10 AM, Simon.Chapman <simon.chapman@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@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