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... > > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
