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
    surface
    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.

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#contactArea

    Tom

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