[PyMOL] Low resolution surface of large structures

[Yuxing L. <Yux...@UT...>]

Hi all,

I was trying to show low resolution surface representation for very large structures following the example at http://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.