Hi Carsten, I appreciate your reply and I would assume that it makes impressive graphics, but it sounds WAY beyond my meager abilities (I am struggling with the Mac OS X version of Pymol after all and haven't ventured into the realm of raster3D yet). I assume that since there has been a resounding lack of response within the Pymol masses that it either can't be done or hasn't been done. Just in case somebody missed the prior posting I would like to be able to perform a selective Z-clipping in order to cross-section an active site pocket with a bound ligand. The challenge comes in trying to Z-clip the protein structure (shown as a "surface" display) while retaining the entire ligand (no Z-clip on the ligand). Prior attempts have either Z-clipped everything (create protein as an object, create ligand as an object, then Z-clip) or Z-clipped nothing (create protein as an object, execute the Z-clip, then create ligand as an object and display it). Somehow the creation of the ligand as an object and displaying it over-rides the prior Z-clip and both objects are displayed in their entirety.
Any suggestion within the Pymol world? Thanks, Kelley On 11/25/02 3:06 PM, "pymol-users-requ...@lists.sourceforge.net" <pymol-users-requ...@lists.sourceforge.net> wrote: > --__--__-- > > Message: 1 > From: "Schubert, Carsten" <carsten.schub...@3dp.com> > To: "'Kelley Moremen'" <more...@arches.uga.edu>, > pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] Selective Z-clipping > Date: Mon, 25 Nov 2002 09:07:13 -0500 > > Hi Kelley, > > I just worked out a procedure to do this with VMD/Raster3D (oops, this is > the PyMol list ...). Anyhow, it boils down to that you can apply selective > bounding or clipping planes in Raster3D. In the case of a clipped surface > you want to use a bounding plane, which slices through an object and > produces a sealed cut (bounding plane) or really play with the lights to get > rid of all the interior surfaces exposed by a non-sealing cut with a > clipping plane. I played around a little bit with Povray to achieve the same > effect. I figured out to use an intersection with CGOs but somehow I could > not get it to work with a surface definition. May be somebody else knows how > to do this. I'd be interested in it to. > > Here is what I did. Split your scene into their components and write out the > raster3d input files. Remove all headers from the r3d files and save one > header into a control script (master.r3d) If you use vmd (oops again...) you > have to get rid of the object 17 in the surface definition, otherwise you > will not be able change colors, transparency etc. Use remove_17.pl for this. > The animate_bounding.pl script allows you to move the bounding plane in a > given range to find the right orientation. The only way to do this is by > trial and error. A good starting point is a plane defined by the normal > vector 0,0,1 (x,y plane at origin of scene). > > good luck. > > > Carsten Dr. Kelley Moremen Associate Professor Complex Carbohydrate Research Center Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602-7229 Office (706) 542-1705 Fax: (706) 542-1759 Email: more...@arches.uga.edu (send email with large attachments to: more...@bmb.uga.edu) Website: http://bmbiris.bmb.uga.edu/moremen/lab/
