Some options were posted along these lines but you have to know what to look for since they are under titles like EM-izing your structure.

You can try:
set surface_quality, -3
(I think that's as low as you can go, more negative doesn't get any blobbier).

And a bit less simple but I think you'll prefer the option quoted below from Warren's email reply to that EM-izing question, since you are after "super smooth" not just "smooth" (I found setting the gaussian_resolution to 13 or so to be in the "super" realm and don't forget to add a fourth argument to the map_new bit if you want that as mentioned below):
alter all, b=10

map_new can take a selection as its fourth argument, so you could
generate an independent map for each subunit, show the surface, and
color it independently. It's also possible to color a surface by atomic
proximity, but the approach is a bit convoluted:

load some.pdb, prot
util.cbc prot
alter prot,b=10
set gaussian_resolution, 9.0
map_new dcalc, gaussian, 3.0
map_double dcalc
isosurface dsurf, dcalc, 1.0, prot

End Quote

Hope that's what you're after.

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   3. Super-smooth surfaces (Stephen Graham)
Message: 3
Date: Wed, 11 Jan 2006 22:22:15 +0000
From: Stephen Graham <>
Subject: [PyMOL] Super-smooth surfaces

Hi there,

I am making a figure in which I would like an extremely smooth
molecular surface (I just want the protein as a blob with little to no
definition of surface features).

I tried setting the probe radius to a larger value:
set solvent_radius, 8
but this gives rise to ugly artefacts on the surface ('triangles' of
surface seem to be missing).  There seems to be a whole raft of
different settings for fine-tuning surfaces (surface_carve_*,
surface_trim_*, etc) but I am afraid I do not know what they do and
have been unable to find documentation on them.

How can I make a surface happy (fully connected) after having set the
probe radius way up?



Stephen Graham
Crystallography Group
School of Molecular and Microbial Biosciences
University of Sydney

End of PyMOL-users Digest