Igor is right. However, there is a new command in recent versions
map_double map-name
that will cut the map spacing in half by interpolating a new map via
trilinear interpolation. This will generate a map with 2^3 = 8-fold
more grid points (and require 8X more RAM!)
load map1.ccp4
map_double map1
isomesh mesh1, map1, 1.0
will generate a mesh with half the spacing of the original map.
Note that map_double can usually only be used once on a given map before
averaging artifacts appear.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
ad...@lists.sourceforge.net] On Behalf Of Igor Pechersky
Sent: Tuesday, November 25, 2003 7:23 AM
To: mwilke
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] electron density settings
mwilke mwi...@interchange.ubc.ca:
Does anyone know how to alter the isomesh settings? I'm trying to
prepare
a figure with pretty electron density and would like to be able to
decrease
the gap size of the mesh. I found the variables that seem to make
sense
like mesh_quality and min_mesh_spacing, but changing these
variables
doesn't seem to do anything. mesh_width and mesh_radius only
control
the thickness of the mesh lines.
Mark,
you are correct, saying that mesh_quality and min_mesh_spacing
have
nothing with
isomesh. They are used only for surface maps (RepMesh). For map-based
mesh, PyMOL uses
dimension from the density map itself, without smoothing
interpolations.
So, to
increase visual toughness of your isomesh, you should just load more
fine-grained
density map...
As a visualization trick, one might try to play with the set of
isomeshes, based on
the same density map and slightly differentiated by level, like this:
isomesh mesh1, map1, 1.0
isomesh mesh2, map1, 1.25
isomesh mesh3, map1, 1.50
isomesh mesh4, map1, 1.75
isomesh mesh5, map1, 2.0
and then color them differently.
BTW, even with RepMesh you can't decrease gap size (via
min_mesh_spacing)
less than
some hard lower threshold - roughly, it is equivalent to 80 lines
per
maximal
dimension of the surrounding box for the underlying object.
mesh_quality deals rather with the level of icosahedron approximations
for
spheres...
---
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