Hi Stephen 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 alter my_protein, vdw=4 sort 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. Cheers Esben > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Stephen Graham > Sent: 11. januar 2006 23:22 > 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 > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep > through log files for problems? Stop! Download the new AJAX > search engine that makes searching your log files as easy as > surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_idv37&alloc_id865> &op=ick > > _______________________________________________ > > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
