this works for me. You have to specify either buffer or carve with "named variables" (hope that is the right term). inh1 is the selection I defined the map to be centered on.
# load maps
load 2fofc.ccp4, 2fofc_map
load fofc.ccp4, fofc_map
isomesh 2fofc, 2fofc_map, 1.4, inh1, carve=2
color marine, 2fofc
isomesh fofc1, fofc_map, 3.0, inh1, buffer=2
color forest, fofc1
isomesh fofc2, fofc_map, -3.0, inh1, buffer=2
color firebrick, fofc2
Hope it helps
From: Rongjin Guan [mailto:firstname.lastname@example.org]
Sent: Tuesday, January 14, 2003 11:22
Subject: [PyMOL] how to control the density coverage in pymol
I am new to this BB.
In O we can use something like "map_cover object radius" to only
display the density aroung the part model we are interested, and get
rid of other densities neaby to make the figure "clean".
But in PyMOL, I tried "insomesh den, map1, 1.0, (i;8,9), 3.0" to try
to only display the density around residues 8 and 9, but there are
still some additional densities neaby, which makes the figure a little
"dirty". Anybody has some ideas to deal with it?
Rongjin Guan, Ph.D.
Center for Advanced Research in Biotechnology
9600 Gudelsky Drive
Rockville MD, 20850