Hi Elaine, yes the centroid option is what I would like to do for each aromatic ring. The thing is that I have a small database to screen regarding relative position of this centroids. My main problem is how could I generate automatically a unique group of atoms for each ring and then calculate the centroid afterwards. I have no idea. Thanks for the help, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: Elaine Meng <meng@cgl.ucsf.edu> Data: Dissabte, Febrer 13, 2010 8:31 pm Assumpte: Re: [chimera-dev] No glue!

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/struc...

...

<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@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