[Chimera-users] Depicting buried surfaces

Tom Goddard goddard at sonic.net
Thu Oct 11 18:31:28 PDT 2012

> Hi Tom,
> I have a non-EM density question!
> Is there a way to display the buried surface between two PDB chains in Chimera? Something like what GRASP does:
> http://www.csb.yale.edu/poststructure/grasp/grasp2.html
> I know I can measure the area with:
> "measure buriedArea :.A :.B"
> but is there a way to display the buried surfaces?
> Thanks!
> -gabe

Hi Gabe,

    The measure buriedArea command sets a value for each atom giving the
area buried (square Angstroms).  So you can use

      measure buriedArea :.A :.B
      surfcat a :.A
      surfcat b :.B
      color pink :.A
      color lightblue :.B
      surface @/buriedSESArea>1

The surfcat command just defines chains A and B as two different objects
for surfacing and the surface command show the surface patches
associated with all atoms having buried solvent excluded surface area
greater than 1 square Angstrom.  It shows the entire patch of area for
those atoms, not just the part that is buried. So it is pretty ugly and
a bigger surface then just the buried part.

    For a much prettier picture but a slightly different measurement you
might try instead

      split #0
      measure contactArea #0.1 #0.2 2 slab 0.5

The split puts chains A and B in two models #0.1 and #0.2.  The
"surface" makes surfaces on each.  And the "measure contactArea..."
finds all points on one surface within 2 Angstroms of any point on the
other surface and displays a pretty looking slab depicting the surface
(attached picture).  This is a different definition of buried area but
might do.



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