[Chimera-users] seelction around map

Tom Goddard goddard at cgl.ucsf.edu
Fri Sep 7 16:53:09 PDT 2007

Hi Dhiraj,

  Ah, ok you have a map of the cavity created by voidoo.  So you could 
use the "distance to surface" Chimera plugin I mentioned, make a small 
addition to the code to select the atoms close to the surface (rather 
than just print the distances).  All in all it would be more work and 
give a slightly different results I think than the cavity surface 
residues listed by voidoo.  Also this Chimera code is all in Python and 
is quite slow, so the distance to the surface calculation takes some 
seconds per atom for protein size surfaces, and that could take some 
time to calculate for thousands of atoms in your channel.  If you wanted 
to try it nonetheless, you would add two lines of code to the "distance 
to surface" plugin, file SurfaceDistance/surfdist.py, line 32, just 
before the line

            for a, dmin, sxyz, side in dlist:

put in two lines as follows:

            from chimera.selection import setCurrent
            setCurrent([a for a,dmin,sxyz,side in dlist if dmin <= 3.2])

You need the same indentation because that is important in Python.


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