From: Thomas H. <tho...@sc...> - 2015-02-12 22:43:05
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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 <Yux...@UT...> 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. |