How large is large?
With enough RAM, PyMOL can do molecular surfaces up to perhap a hundred
thousand atoms or so, but above that, you probably need to fall back on
Gaussians as illustrated in the script below:
Cheers,
Warren
# load a whopping big PDB
load one_million_atoms.pdb, struct
spectrum count, selection=struct
# give ourselves a responsive UI
as spheres
set sphere_mode,1
# === now create a pseudo-fcalc map (a 3D volumetric scalar field) ===
# set the B-factors nice and high for smoothness
alter all, b=40
# ~10 A map resolution
set gaussian_resolution, 10
# ~10 A map spacing with a 10 A surrounding buffer
# (you may need to vary this)
map_new map, gaussian, 10, struct, 10
# create a surface from the map
isosurface surf, map, 1.0
# now color the map based on the underlying protein
ramp_new ramp, struct, [0,10,10], [-1,-1,0]
color ramp, surf
disable ramp
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...
> -----Original Message-----
> From: Crystal K. Chuang [mailto:CKC...@lb...]
> Sent: Tuesday, December 16, 2008 5:11 PM
> To: pym...@li...
> Subject: [PyMOL] PyMol memory vs. computer memory
>
> Hello,
>
> When I try to add a surface to a very large structure and
> PyMol gives me the error message "PyMol just ran out of
> memory and crashed...." am I receiving this message due to
> limitations of the PyMol program, or do I need to install
> more memory on my computer?
>
> Thanks
> -Crystal
>
>
>
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