[Chimera-users] Distance between two benzene rings

[Elaine Meng]

Hi George,
You can define centroids for the rings and then measure the distance between those centroid objects.  See "Axes/Planes/Centroids" (under Tools... Structure Analysis) and/or command "define":
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

The objects you have defined will be listed in a dialog, and you can measure distance simply by choosing two objects (rows) in the dialog, or by using the "distance" command.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#objectlist>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>

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 Sep 6, 2012, at 2:26 AM, George Tzotzos wrote:

> Hi everybody,
> 
> I'm trying to work out stacking interactions between two benzene rings. Is there a way to measure the distance from the center of the benzene rings of a Tyr to the center of the benzene ring of a Phe residue?
> 
> Your help suggestions / help much appreciated as always
> 
> Regards
> 
> George
> 
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