Re: [PyMOL] PyMol memory vs. computer memory

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


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> -----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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