[Chimera-users] Coordinates

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 1 09:50:32 PDT 2011

On second thought, better stick with "define centroid" (method B) for now, as experiments suggest that method A is giving the transformed coordinates, i.e. different answers after you rotate or translate the structure.


On Jul 1, 2011, at 9:30 AM, Elaine Meng wrote:

> Hi George,
> There are at least a couple of possibilities.
> (A) the command "measure inertia" -- the mass-weighted center of the specified atoms will be reported in the Reply Log along with other stuff.  You can specify any set of atoms. It creates an ellipsoid by default but there is an option to turn that off.  For example:
> measure inertia :47.a
> (residue 47 in chain A)
> measure inertia protein showEllipsoid false
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> (B) if you want to show a sphere at the centroid, the command "define centroid" -- again, any set of atoms can be specified, and the center is reported in the Reply Log.  In this case, mass weighting is an option, default false (thus giving center of geometry).  For example:
> define centroid mass true radius 1.5 color cyan :47.a
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>
> I hope this helps,
> 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 1, 2011, at 9:05 AM, George Tzotzos wrote:
>> Hi everybody,
>> Is there a way to find out the coordinates of the centre of mass of (a) protein; (b) a specific residue in a protein; (c) a ligand bound on a protein. I searched the Chimera documentation but didn't find anything appropriate. Maybe that my search terms were wrong.
>> Many thanks and best regards
>> George
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