[Chimera-users] [chimera-dev] adding an atom at the centroid of a blob

Jean Didier Pie Marechal JeanDidier.Marechal at uab.cat
Thu Jan 14 11:53:57 PST 2010

Thanks a lot Elaine for answering me, I was indeed interested in both user interfase ...as well as the python shell one...


Dr. Jean-Didier Maréchal
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: Dimecres, Gener 13, 2010 11:26 pm
Assumpte: Re: [chimera-dev] adding an atom at the centroid of a blob

> On Jan 13, 2010, at 8:01 AM, Jean Didier Pie Marechal wrote:
> > Hi everyone,
> > I have obtained cavities for a given atom selection using surfnet 
> > and I want to put an atom at the centroid of the main blob. I 
> know  
> > how to do this for a selected set of atom but I am struggling 
> with  
> > the surfaces.
> >
> > At this point, I splitted it (accelator Sc) and then I can select 
> > the blob I am interested in. But how could I create a particular  
> > object for this blob? From there, how could I add an atom (i.e.  
> > helium) and the centroid of the blob?
> > Thanks for any help,
> > JD
> Hi JD,
> Now that you have your one surface piece selected (and nothing 
> else),  
> you could use the command "focus sel" or menu item "Actions.. 
> Focus"  
> to center the view on it, then add the atom at the center of view  
> with the Build Structure tool (under Tools... Structure Editing).   
> You would go to the "Add Atoms" tab in that tool, choose "atom" and 
> click "Add."
> It may not be the centroid of the blob as calculated from its  
> vertices, but the center of its bounding box.  You may want to try 
> it  
> and see if the result is sufficient.
> That's the user interface way.  Maybe you meant in python -- if so, 
> somebody else will have to answer!
> Best,
> Elaine

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