[Chimera-users] An ellipsoid around a protein

[Elaine Meng]

Dear M,
Chimera questions should be sent to chimera-users at cgl.ucsf.edu (CC'd here).

In Chimera you can calculate and display the inertia ellispoid for any set of atoms with the command "measure inertia."  For example, you could open the protein structure in Chimera, show the command line (from Favorites menu) and then enter the command:

measure inertia protein

The principal axis information is given in the Reply Log. There are other keywords, such as to control the color of the ellipsoid.  See:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia>

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 May 29, 2011, at 9:45 PM, mselvaraj at mbu.iisc.ernet.in wrote:

> Dear sir,
>    I would like to calcualte an ellipsoid with its principle axis for a 
> protein molecule,given its PDB.  I came across your discussion on
> chimera-users discussion.. Do you have a program that can calculate the
> ellipsoid and its principle axes.  It would be very help ful for my
> analysis.  Thanks in advance.
> 
> yours sincerely,
> M. Selvaraj,
> Graduate student,
> Molecular Biophysis Unit,
> Indian Institute of Science,
> Bangalore 560 012
>