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 :
> > 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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