Re: [PyMOL] Low resolution surface of large structures

[Thomas H. <tho...@sc...>]

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.