[Chimera-users] calculating centroid of atoms

David Chenoweth dchen at caltech.edu
Thu Apr 2 09:01:56 PDT 2009

Hi Bala,

I have been using the free program Mercury to calculate centroids. It  
allows you to pick any number of atoms, least-squares fit them to a  
plane, and calculate a centroid. I usually do this and then output the  
xyz coordinates  and past them into a pdb file with a dummy atom name  
or you can assign the atoms to boron or something else not in your  
structure. You can then open your pdb files and use chimera to  
superimpose centroid atoms of multiple structures or make measurements  
and pictures. Mercury also allows you to least squares fit planes to  
atoms or points and measure angles between intersecting planes. These  
would be great analysis tools to add to Chimera! If you need any help  
or more info don't hesitate to email me.


David M. Chenoweth
California Institute of Technology
Division of Chemistry and Chemical Engineering
Mail Code: 164-30
1200 California Boulevard, 91125 Pasadena
California, USA

Phone: 626-395-6074
Email: dchen at caltech.edu

On Apr 2, 2009, at 1:06 AM, Bala subramanian wrote:

> Friends,
> I want to choose certains atoms and get the x,y,z coordinates of the  
> center. Kindly write me how to do it in chimera.
> Bala
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