Try a command sequence like this: alter all,b=10 set gaussian_resolution, 9.0 map_new dcalc, gaussian, 3.0 map_double dcalc isosurface dsurf, dcalc, 1.0
Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Andreas Förster > Sent: Wednesday, November 30, 2005 1:32 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] EMizing an xray structure > > Hey all, > > I'm trying to make a figure from a pdb that's supposed to > look like an EM structure. According to an older post from > Warren I should increase solvent_radius and alter vdw. > > For most combinations of the two, artefacts appear all over > the place, like missing surface and surface floating about. > I succeeded in making a figure without artifacts (high vdw > increase, minimal solvent_radius increase), but it looks more > like a lychee than a protein. > > Has anyone found numbers that work well? Or a different > approach to creating an EM reconstruction-like figure. > > Merci bien. > > > Andreas > > > > -- > --> Andreas Förster <-- > Institut de Biologie Structural, Grenoble > www.biochem.utah.edu/~andreas > > > ------------------------------------------------------- > 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/pymol-users > > > >
