RE: [PyMOL] electron density settings

[Warren L. D. <wa...@de...>]

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:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Igor Pechersky
> Sent: Tuesday, November 25, 2003 7:23 AM
> To: mwilke
> Cc: pym...@li...
> Subject: Re: [PyMOL] electron density settings
> 
>  mwilke <mw...@in...>:
> > 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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