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

[Eric Pettersen]

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?

	So, how accurate do you want to be?  You could iterate through the  
coordinates of the surface vertices to compute a centroid.  You would  
probably want to look at the code of the ESP extension for that since  
it gets the coordinates of surface vertices so it can compute the  
electrostatic potential for them.
	My preferred (lazier) approach is to place the atom at the center of  
the bounding sphere, which is where the focus/window commands place  
the center of the view.  Cribbed and modifying code from those  
commands...

from Midas import boundingSphere
from chimera import selection
sph = boundingSphere(selection.copyCurrent())
if sph is None:
	raise ValueError("Nothing selected")
from BuildStructure import placeHelium
a = placeHelium("CTR", position=sph.center)

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu



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