Dieter, Slices are a relatively new feature only found in the beta versions:
http://delsci.com/beta http://delsci.com/macbeta Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . 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 > dieter blaas > Sent: Friday, January 28, 2005 1:19 AM > To: pymol-users@lists.sourceforge.net > Cc: Warren DeLano > Subject: RE: [PyMOL] electron density map manipulation > > Thanx Warren, perfect! But when entering: > > "> load map1.dsn6 > > slice_new slice1,map1 > > I get the message: > Syntax Error: invalid syntax with a ^ pointing to the "1" in > slice1 I have tried several permutations of the syntax, but > always receive an error message! > On 27 Jan 2005 at 22:51, Warren DeLano wrote: > > > > 1/ can I make a solid surface? > > > > Solid (opaque) surface with isosurface command (just like isomesh) > > > > > 2/ can I make volume slices? > > > > Slices are possible: > > > > load map1.dsn6 > > slice_new slice1,map1 > > ramp_new ramp1,map1 > > color ramp1, slice1 > > > > Then ctrl-middle-click and drag to change slice contour coloring > > > > > 3/ can I load the map in the same way I load pdb files without > > > command line input and manipulate the parameters with the mouse? > > > > Not yet. > > > > > is it O.K. to answer in this way or should I send the mail to the > > > mailing list? > > > > The mailing list is preferable. > > > > Cheers, > > Warren > > > > > > -- > > Warren L. DeLano, Ph.D. > > Principal Scientist > > > > . DeLano Scientific LLC > > . 400 Oyster Point Blvd., Suite 213 > > . South San Francisco, CA 94080 > > . Biz:(650)-872-0942 Tech:(650)-872-0834 > > . Fax:(650)-872-0273 Cell:(650)-346-1154 > > . mailto:war...@delsci.com > > > > > > > -----Original Message----- > > > From: dieter blaas [mailto:dieter.bl...@univie.ac.at] > > > Sent: Thursday, January 27, 2005 9:20 PM > > > To: Warren DeLano > > > Subject: RE: [PyMOL] electron density map manipulation > > > > > > Thanx a lot, this works! I have three additional questions: > > > 1/ can I make a solid surface? > > > 2/ can I make volume slices? > > > 3/ can I load the map in the same way I load pdb files without > > > command line input and manipulate the parameters with the mouse? > > > > > > is it O.K. to answer in this way or should I send the mail to the > > > mailing list? > > > Dieter > > > > > > > > > On 27 Jan 2005 at 16:49, Warren DeLano wrote: > > > > > > > Dieter, > > > > > > > > Have you tried the isomesh and isosurf commands? > > > > > > > > load map1.dsn6, map1 > > > > isomesh mesh1, map1, 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 > > > > . 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 > > > > > Dieter Blaas > > > > > Sent: Monday, January 24, 2005 6:54 AM > > > > > To: pymol-users@lists.sourceforge.net > > > > > Subject: [PyMOL] electron density map manipulation > > > > > > > > > > Hi, I have been trying to visualize a DN6 electron > density map. > > > > > Although it is read in apparently correctly nothing > shows on the > > > > > screen. Are there any particular parameters to be set? I can > > > > > visualize it in SwisspdbViewer but I was unable to produce > > > > > surface rendering. Can Pymol produce a surface at a > particular > > > > > cut-off value as can Amira? > > > > > Thanx for hints, Dieter > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > > > > > Reporting Tool for open source databases. Create drag-&-drop > > > > > reports. Save time by over 75%! Publish reports on the web. > > > > > Export to DOC, XLS, RTF, etc. > > > > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > > > > > _______________________________________________ > > > > > PyMOL-users mailing list > > > > > PyMOL-users@lists.sourceforge.net > > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > > > > > > > > > > > > > > > >
