[Chimera-users] Principal axis of inertia

Tom Goddard goddard at cgl.ucsf.edu
Fri May 15 10:40:39 PDT 2009

Hi Armida,

  Elaine is right.  The atoms are weighted by their mass, carbon counts 
12 times more than a hydrogen.  Isotopic abundances are not considered 
-- I think Chimera's atom.element.mass is just the number of protons 
plus neutrons in the post prevalent isotope.  It is not too surprising 
that the inertia ellipsoid comes out nearly identical for CA only versus 
all atoms for a protein.  The CA atoms give a good approximation to the 
mass distribution.  The main difference is that the total mass will be 
different, but that is normalized out in the ellipsoid calculation.


Elaine Meng wrote:
> 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  
> "a.element.mass":
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080321/21f01cdf/attachment.ksh 
>  >
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html 
>  >
> 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.
> Best,
> Elaine
> -----
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 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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