[chimera-dev] No glue!

[Elaine Meng]

Hi JD,
I can't answer in terms of programming, but thought I would mention  
that in recent daily builds (version 1.5), "Axes/Planes" (under  
Tools... Structure Analysis) has been extended to "Axes/Planes/ 
Centroids."  With this tool, or with the command "define," you can  
create a sphere at the optionally mass-weighted centroid of any set of  
atoms.

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

These centroid objects, although not atoms, can be used in distance  
measurements via the "Axes/Planes/Centroids" GUI or with the command  
"distance."

Perhaps these centroid objects will meet your needs, so you don't need  
to write this code to create atoms.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Feb 13, 2010, at 6:25 AM, Jean Didier Pie Marechal wrote:

> Dear all,
> I'd like to add an atom at the mass center of each aromatic fragment  
> of my ligand (I always want to add an atom don't I?).
>
> I know how to calculate cm, put an atom or point, select aromatic  
> ring BUT I am banging my head against the wall to define one entity  
> of each ring separately.
>
> Would it be a lot more complicate to do so for any cyclic moeity.
> Thanks for any help!
> best,
> JD