> From: Vajdos, Felix [mailto:felix_vajdos@...]
> Does the "carve" option in contouring map objects actually=20
> work? I would
> like to display e-density only around my ligand, but no=20
> matter what value I
> set [carve] to, I get density from surrounding residues displayed:
> isomesh map1, map, 2, (resn PFE), 1
> give the same result as
> isomesh map1, map, 2, (resn PFE), 1, 1, 1.
> I would like to display only the density around the object=20
> (analogous to the
> map_cover command in O).
> Any suggestions?
It should work -- you might not want to specify a buffer, since carve
effectively replaces it. Literally:
isomesh map1, map, 2, (resn PFE), carve =3D 0.5
Gradually increase carve until you get the density you want -- 1.5 to
2.0 is usually about right.
Remember that the cutoff is geometric -- it doesn't know where the
density is coming from. What you're effectively doing is carving out a
collection of spheres in the map about your atom selection.
Warren L. DeLano, Ph.D.
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
> Felix F. Vajdos
> Pfizer Inc
> Eastern Point Road
> MS 4039
> Groton, CT 06340
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