> From: Vajdos, Felix [mailto:felix_vaj...@groton.pfizer.com]
Hi Felix!
> Does the "carve" option in contouring map objects actually
> work? I would
> like to display e-density only around my ligand, but no
> 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
>
> is
>
> isomesh map1, map, 2, (resn PFE), 1, 1, 1.
>
> I would like to display only the density around the object
> (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 = 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
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
>
> Thanks!
> Felix
>
>
> Felix F. Vajdos
> Pfizer Inc
> Eastern Point Road
> MS 4039
> Groton, CT 06340
>
> 860-715-6504
>
>
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