From: Igor P. <igo...@pi...> - 2003-11-25 15:23:29
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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... |
From: Warren L. D. <wa...@de...> - 2003-11-25 18:19:20
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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... > > > > ------------------------------------------------------- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Robert <ro...@sd...> - 2003-12-10 22:59:08
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Hi there, 1. How can I reduce the density-map line thickness in the ray-traced image? 2. Is there a way to just display the density around a ligand many thanks robert Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637 |
From: Warren L. D. <wa...@de...> - 2003-12-10 23:27:40
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Robert, If you're using version 0.93 or greater, set mesh_width, value will adjust the mesh thickness in units of pixels. Something in the range of 1.5-2.5 usually works best. set mesh_width,2.0 ray If you're using an older version, you'll need to set mesh_radius instead, which is in angstrom units. To display the density around a ligand, create a mesh using the "carve" option. load map.ccp4 load protein.pdb load ligand.pdb isomesh m1, map, 1.0, ligand, carve=2.1 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 Robert > Sent: Wednesday, December 10, 2003 2:55 PM > To: 'Warren L. DeLano' > Cc: pym...@li... > Subject: [PyMOL] electron density settings > > Hi there, > > 1. How can I reduce the density-map line thickness in the ray-traced > image? > 2. Is there a way to just display the density around a ligand > > many thanks > robert > > Robert Schwarzenbacher, PhD > The Joint Center for Structural Genomics > phone: 858 822 3637 > > > > > > ------------------------------------------------------- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |