RE: [PyMOL] electron density settings
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: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 Robert Sent: Wednesday, December 10, 2003 2:55 PM To: 'Warren L. DeLano' Cc: pymol-users@lists.sourceforge.net 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 PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
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...
RE: [PyMOL] electron density settings
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
