Kelley,
Unfortunately PyMOL doesn't have object-specific Z-clip. (That is a
cool idea though, perhaps in the future...)
The closest thing to this you can accomplish is to selectively show or
hide the surface on certain atoms in order to create a view which shows the
full ligand and only part of the surface. This would be a lot of work though,
so I can't recommend it.
Sorry,
Warren
> -----Original Message-----
> From: Kelley Moremen [mailto:more...@arches.uga.edu]
> Sent: Monday, November 25, 2002 2:03 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #218 - 1 msg
>
>
> 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/
>
>
>
>
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