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

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 13 14:26:37 PST 2010

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!



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