[Chimera-users] Depicting buried surfaces

Eric Pettersen pett at cgl.ucsf.edu
Fri Oct 12 15:58:19 PDT 2012

A related tool in Chimera is Intersurf, for showing interface surfaces:



                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Oct 11, 2012, at 6:31 PM, Tom Goddard wrote:

>> 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
> <contactArea.jpg>_______________________________________________
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