Re: [PyMOL] Surface Edge

[<Mat...@im...>]

pym...@li... wrote on 09/20/2006 07:28:00 AM:

> Paul,
>
>  I think the reason the surface coloring "spills over" is because
> there are some surface triangles that are shared by the selection you
> want (red) and the neighboring residues (grey)...  So it should work
> if you only use one selection, by saying something like:
> load my_protein.pdb,
> show surface,
> color grey,
> color red, (something at the center of the pocket) expand 8
>
> Hope this helps,
>
> -bob
>

I think this is the right approach.  If you invert the selection for the
other surface, you should be able to avoid having triangles in both
surfaces.  Like this:

load my_protein.pdb
create pocket, chain a
create rest_of_protein, chain a
color red, pocket
color gray, rest_of_protein
show surface, pocket and resi 10-15
show surface, rest_of_protein and not(resi 10-15)
set transparency=0.5, rest_of_protein

This gave a sharp edge when I just tried it.  If you don't like the jagged
look of the edge, try changing the color statements above, to

color gray, pocket
color red, pocket and resi 10-15
color gray, rest_of_protein

Now your red triangles will fade into the semi-transparent gray surface.

Hope that helps,

Matt

--
Matthew Franklin                     phone:(917)606-4116
Senior Scientist, ImClone Systems      fax:(212)645-2054
180 Varick Street, 6th floor
New York, NY 10014


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