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):
Quote:::
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.
-Seth
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 3. Super-smooth surfaces (Stephen Graham)
> _
> Message: 3
> Date: Wed, 11 Jan 2006 22:22:15 +0000
> From: Stephen Graham <steph...@usyd.edu.au>
> To: pymol-users@lists.sourceforge.net
> 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?
>
> Thanks,
>
> Stephen
>
> --
> Stephen Graham
> Crystallography Group
> School of Molecular and Microbial Biosciences
> University of Sydney
>
>
> End of PyMOL-users Digest
>
