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
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Jean Didier Pie Marechal