[gmx-users] Finding centroid for a bunch of residues

Steven Kirk steven.kirk at hv.se
Mon Oct 6 14:55:56 CEST 2008

> Hi there,
> This is the question out of gromacs..but I need it urgently.. and I hope
> this is the only place where I can get such expert to solve my query...
> while trying to restrict my MDRUN for a particular site of the protein
> molecule I want to visualize the site and find out the centroid for the
> particular site......
> Is there any visualization tool that can do the same ..
> I mean Is there any molecular visualization tool that can help in finding
> out the ...centroid between a group of resuidues ?

Pymol has a script that computes the center of mass for a selection, and 
optionally, moves this center of mass to the origin:


Haven't used it myself, so I can't vouch for its effectiveness.

Steve Kirk
Dr. Steven R. Kirk           <steven.kirk at hv.se, S.R.Kirk at physics.org>
Dept. of Technology, Mathematics & Computer Science  (P)+46 520 223215
University West                                      (F)+46 520 223299
Trollhattan 461 86 SWEDEN                     http://beacon.webhop.org

More information about the gromacs.org_gmx-users mailing list