[Chimera-users] Depicting buried surfaces
pett at cgl.ucsf.edu
Fri Oct 12 15:58:19 PDT 2012
A related tool in Chimera is Intersurf, for showing interface surfaces:
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:
>> I know I can measure the area with:
>> "measure buriedArea :.A :.B"
>> but is there a way to display the buried surfaces?
> 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.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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