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