RE: [PyMOL] Surface of cavity

Paul,

PyMOL generally shows all sides of an exposed atom, but perhaps you
could load both the GOLD output and the original structure.

You could then only show the surface on the atoms in the original
structure with corresponding atoms in the gold output as follows:

load orig.pdb
load gold.pdb

then=20

show surface, orig in gold

or

show surface, orig like gold

That might produce something close to what you want.  Note that:

"in" matches chains, segments, residue names, residue ids, and atom
names.

"like" just matches residue ids and atom names.

You can use

alter all, segi=3D''
alter all, chain=3D''

to clear out the segment and/or chain IDs before using "in" to
selectively reduce its stringency.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Paul Wilhelm Elsinghorst
> Sent: Friday, January 20, 2006 11:33 PM
> To: pym...@li...
> Subject: [PyMOL] Surface of cavity
>=20
> Hi,
>=20
>=20
> a little question regarding cavity surfaces :-)
>=20
>=20
> I have a set of active atoms (GOLD output) that surround a=20
> cavity. Now I want to dipslay the surface only for the cavity=20
> wall, not on the outside.
>=20
>=20
> Any ideas?
>=20
>=20
> Paul=20
>=20