Below is an example script demonstrating how to create low-resolution
structure "blobs" using PyMOL:
load $TUT/1hpv.pdb, inp
remove not polymer
alter all, b=50
alter all, q=1
map_new mapA, gaussian, 1, inp and chain A, 6
isosurface surfA, mapA
set gaussian_resolution, 8
map_new mapB, gaussian, 2, inp and chain B, 10
isosurface surfB, mapB
color wheat, surfA
color teal, surfB
Note that the temperature factor field (b) has at least as much impact as
the resolution setting, so in practice, increasing b factors is the more
computationally efficient way of increasing the blur effect.
DeLano Scientific LLC
Subscriber Support Services
[mailto:pymol-users-bounces@...] On Behalf Of Pietro
Sent: Thursday, September 11, 2008 5:18 AM
Subject: [PyMOL] I want to represent a domain of my molecule as a
lowresolution solid shape
I want to represent a domain of my molecule as a low
resolution solid shape.
I have chosen surface representation but the surface is clipped, exposing
the inner part, which makes the domain appear hollow. The rendering of the
inner surface appears greyish and different from the outer part.
Can I make the clipped surface filled so that this greyish inner part is not
there anymore? It should look solid inside.
Alternatively, do you think I should switch to spheres representation?
But I still would need to blur the spheres to achieve the low-resolution
look of the domain.
Thanks for any suggestions you can provide!
Sir William Dunn School of Pathology, Oxford University South Parks Road,
Oxford OX1 3RE, England UK Tel. 0044-1865-275385
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