I also use smooth surfaces - for visualizing results from small angle
xray scattering, which is a low resolution technique. I use:
set solvent_radius, 4 =20
alter my_protein, vdw=3D4=20
show surface, my_protein
Maybe you can set solvent_radius a little bit higher, but not much, as
you will get "holes" in the surface like you see. You can adjust the
"blobbiness" by changing the vdw size.
> -----Original Message-----
> From: pymol-users-admin@...
> [mailto:pymol-users-admin@...] On Behalf Of=20
> Stephen Graham
> Sent: 11. januar 2006 23:22
> To: pymol-users@...
> Subject: [PyMOL] Super-smooth surfaces
> Hi there,
> I am making a figure in which I would like an extremely=20
> smooth molecular surface (I just want the protein as a blob=20
> 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=20
> ('triangles' of surface seem to be missing). There seems to=20
> be a whole raft of different settings for fine-tuning=20
> surfaces (surface_carve_*, surface_trim_*, etc) but I am=20
> afraid I do not know what they do and have been unable to=20
> find documentation on them.
> How can I make a surface happy (fully connected) after having=20
> set the probe radius way up?
> Stephen Graham
> Crystallography Group
> School of Molecular and Microbial Biosciences
> University of Sydney
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