[Chimera-users] RMSD

Valerio Chiarini valerio.chiarini at helsinki.fi
Fri Jul 17 07:32:52 PDT 2015


Thnk you very much Elaine, I will take the values from Amber output directly.

Thank you very much

Val
Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> 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
> -----
> 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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