[chimera-dev] No glue!

[Jean Didier Pie Marechal]

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 at uab.es

----- Missatge original -----
De: Elaine Meng <meng at 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/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
>