Re: [PyMOL] electron density settings

[Igor P. <igo...@pi...>]

 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...