[Chimera-users] RMSD

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 17 07:05:41 PDT 2015


Hi Val,
Chimera does not calculate an “ideal geometry” for a structure.  As far as I know, there is no single ideal that everybody would agree upon anyway.  

Also, I’m guessing that this "RMSD from the ideal" reported in papers might not be for XYZ coordinates.  It might be that the authors have a list of ideal torsion angles (again, I doubt there are values everybody would agree on) and are calculating the RMSD of the angles in the structure versus the values in that list.  It’s just a guess, however, and Chimera also does not have any option to do that calculation. In any case, the authors should provide more details in their papers.

Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 17, 2015, at 12:47 AM, Valerio Chiarini <valerio.chiarini at helsinki.fi> wrote:

> Hi everyone,
> I am dealing with an NMR structure and I noticed in literature that among the parameters required for presentation is included "RMSD from the ideal geometry". Does anyone know if is possible to calculate such value from chimera and how? Currently I just know how to calculate RMSD to the mean coordinate...
> thank you all in advance
> Val




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