[Chimera-users] question about surface properties in Chimera

[Elaine Meng]

Hi Katie,
For identifying surface residues, please see this previous post:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html>

For residue locations relative to the center of mass, you could first calculate a centroid using the Axes/Planes/Centroids tool (under Tools... Structure Analysis) or equivalently, the command "define,"
and then use the "distance" command to measure distances between the centroid and each residue.

For example, for commands something like:

define centroid mass true name c1 protein
dist c1 :1.a at ca
dist c1 :2.a at ca
[etc.]

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>

The distances would be reported in the Reply Log (under Favorites in the menu) and you can save Reply Log contents to a file.  You would probably want to make a command file of the distance commands (too tedious to type them individually!).

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 5, 2012, at 9:49 AM, Katherine Klymko wrote:

> Thank you for the help. I have another question: Is it possible to write a file with a list of the amino acids on the surface, and possibly their locations relative to the center of mass of the protein?
> Thank you,
> Katie