[Chimera-users] Principal axis of inertia

Elaine Meng meng at cgl.ucsf.edu
Fri May 15 07:35:20 PDT 2009

Hi Armida,
Yes, I believe it uses masses based on element assignments in  
Chimera.  I didn't write the script, but looking at it I see  


How the element is assigned depends on the input file.  PDB files can  
have an element column, but if that is not present, the atom name is  
used.  In that case, it is important that the atom names be in the  
correct columns, otherwise it is not possible to distinguish calcium  
from carbon named CA.  See discussion of PDB format:

You can doublecheck the element assignments by using "Select...  
Chemistry... element... [etc.]" and seeing if that selects what you  
expect.  You could select carbons and see if that selects the same  
number of atoms as when you select the whole model.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 15, 2009, at 2:38 AM, A. Di Fenza wrote:

> Dear Elaine,
> your guess was perfectly right! Thank you very much for the detailed
> instructions it is the first time I use Chimera and that was what I
> needed, now it works.
> I have a question about the algorithm. As far as I have understood,  
> the
> script looks at the element name, say CA or  N or C, to assign the  
> atom
> mass. So that if I have a pdb made of CA atoms only, the atom masses
> used in the inertia matrix calculation are all the same. Is this  
> right?
> I need to be sure because I calculated with your script the inertia
> matrix for the same protein first with all-atom and then with only the
> CA, and I got that they are very similar although using the same mass
> for all the atoms is a quite big approximation.
> Thank you very much for your help!
> Armida

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