Sarina, I'm not sure where that "3D10" is coming from -- it should simply be the number 10:
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 ramp_new dramp, prot, [-10,0,10] color dramp, dsurf 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 > Sarina Bromberg > Sent: Thursday, December 01, 2005 9:45 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] RE: EMizing an xray structure (Warren DeLano) > > Warren, > These commands (see below) go a long way toward solving the > problem of producing low resolution simple structures for my > textbook project. I have some questions: > > The first command elicits an error: > PyMOL>alter all,b=3D10 > Alter-Error: Aborting on error. Assignment may be incomplete. > File "<string>", line 1 > b=3D10 > ^ > SyntaxError: unexpected EOF while parsing > Alter-Error: Aborting on error. Assignment may be incomplete. > Alter: modified 0 atoms. > > The rest work fine. For a multimeric protein, how do I get > different surface colors on different chains? I tried > selecting the chains and coloring them differently before > running the commands below, but the dsurf object was just one > color. Can I make each chain a different object and add ", > objectname" to each of these commands? > > Thanks! > Sarina > > > Message: 6 > > Subject: RE: [PyMOL] EMizing an xray structure > > Date: Wed, 30 Nov 2005 16:51:07 -0800 > > From: "Warren DeLano" <war...@delsci.com> > > To: =?iso-8859-1?Q?Andreas_F=F6rster?= <andr...@biochem.utah.edu>, > > <pymol-users@lists.sourceforge.net> > > > > > > Try a command sequence like this: > > > > alter all,b=3D10 > > set gaussian_resolution, 9.0 > > map_new dcalc, gaussian, 3.0 > > map_double dcalc > > isosurface dsurf, dcalc, 1.0 > > > > Cheers, > > Warren > > > > ------------------------------------------------------- > 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_id=7637&alloc_id=16865&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
