> 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 > > > LEGAL NOTICE > Unless expressly stated otherwise, this message is > confidential and may be privileged. It is intended for the > addressee(s) only. Access to this E-mail by anyone else is > unauthorized. If you are not an addressee, any disclosure or > copying of the contents of this E-mail or any action taken > (or not taken) in reliance on it is unauthorized and may be > unlawful. If you are not an addressee, please inform the > sender immediately. > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
