Hi Yuxing, 3j3y has no b-factors (they are all 0.0), but the map_new command takes b-factors into account. The solution is, before calling map_new:
PyMOL> set gaussian_b_floor, 50 Cheers, Thomas On 12 Feb 2015, at 16:12, Yuxing Liao <[email protected]> wrote: > Hi all, > > I was trying to show low resolution surface representation for very large > structures following the example > athttp://www.pymolwiki.org/index.php/Huge_surfaces. I was able to do it for > the PDB 1AON using > > PyMOL>fetch 1aon, type=cif > PyMOL>set gaussian_resolution, 10 > PyMOL>map_new map, gaussian, 10, 1aon, 10 > ObjectMap: Map created. > ObjectMap: Computing Gaussian map for 58870 atom positions. > ObjectMap: Normalizing: mean = 1.537536 & stdev = 2.457675. > Executive: object "map" created. > PyMOL>isosurface surf, map, 1.0 > Executive: object "surf" created. > Isosurface: created "surf", setting level to 1.000 > ObjectSurface: updating "surf". > > But for some recent huge structures that are only available in mmCIF format, > like 3J3Y, the isosurface command produces nothing. > > PyMOL>fetch 3j3y, type=cif > PyMOL>set gaussian_resolution, 10 > PyMOL>map_new map, gaussian, 10, 3j3y, 10 > ObjectMap: Map created. > ObjectMap: Computing Gaussian map for 2116800 atom positions. > Executive: object "map" created. > PyMOL>isosurface surf, map, 1 > > Any ideas? It is run in Pymol 1.7.4.0 on a computer with Windows 7 and 4GB > memory. Thanks. > > Yuxing Liao > > UT Southwestern > > Medical Center > > The future of medicine, today. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
