[Chimera-users] center of the molecule

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 10 10:46:42 PDT 2009

Hi Bala,
I'm sure this is done several places in the code, but we don't  
currently have user interface centroid calculation (although this is  
planned for the future).  However, I thought of a little trick to get  
the information from Chimera:

(a) select the atoms you want to include in the calculation
(b) command: reset
(c) command: focus sel

Then the center of rotation, reported in the status line and Reply  
Log, will be the geometric (non-mass-weighted) centroid of that set of  
atoms.  It is very important to reset so that the coordinates are not  
transformed from the input file, and then without moving the structure  
yourself, use focus.  If you move the molecule yourself between reset  
and focusing on the selected atoms, the result will be incorrect.

You can test the result by making a little sphere at that position  
(requires recent build, version 1.4) with the shape command and seeing  
if it looks reasonable.  For example,

open 2gbp
select ligand
focus sel
shape sphere center 37.25,30.64,49.52 coord #0 radius 0.4 color red

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. for those who don't mind using fortran programs, I attach a  
little one I wrote a long time ago that prompts the user for an input  
PDB file and then calculates the non-mass-weighted centroid and radius  
of gyration using all the atoms in the file. Caveat emptor.
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On Mar 10, 2009, at 7:08 AM, Bala subramanian wrote:

> Dear Friends,
> How can i get the x,y,z of the center of the loaded molecule in  
> chimera. While i do box generation generation for DOCK program, i  
> want to tell the script to construct box by considering the x,y,z  
> center of the molecule.
> Thanks,
> Bala

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