RE: [PyMOL] Re: PyMOL-users digest, Vol 1 #218 - 1 msg

[DeLano, W. <wa...@su...>]

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:mo...@ar...]
> Sent: Monday, November 25, 2002 2:03 PM
> To: pym...@li...
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #218 - 1 msg
>=20
>=20
> Hi Carsten,
>=20
> I appreciate your reply and I would assume that it makes impressive
> graphics, but it sounds WAY beyond my meager abilities (I am=20
> struggling with
> the Mac OS X version of Pymol after all and haven't ventured=20
> into the realm
> of raster3D yet).  I assume that since there has been a=20
> resounding lack of
> response within the Pymol masses that it either can't be done=20
> or hasn't been
> done. Just in case somebody missed the prior posting I would=20
> like to be able
> to perform a selective Z-clipping in order to cross-section=20
> an active site
> pocket with a bound ligand. The challenge comes in trying to=20
> Z-clip the
> protein structure (shown as a "surface" display) while=20
> 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=20
> 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=20
> over-rides the prior
> Z-clip and both objects are displayed in their entirety.
>=20
> Any suggestion within the Pymol world?
>=20
> Thanks,
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> Kelley
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>=20
>=20
> On 11/25/02 3:06 PM, "pym...@li..."
> <pym...@li...> wrote:
> > --__--__--
> >=20
> > Message: 1
> > From: "Schubert, Carsten" <Car...@3d...>
> > To: "'Kelley Moremen'" <mo...@ar...>,
> >  pym...@li...
> > Subject: RE: [PyMOL] Selective Z-clipping
> > Date: Mon, 25 Nov 2002 09:07:13 -0500
> >=20
> > Hi Kelley,
> >=20
> > I just worked out a procedure to do this with VMD/Raster3D=20
> (oops, this is
> > the PyMol list ...). Anyhow, it boils down to that you can=20
> apply selective
> > bounding or clipping planes in Raster3D. In the case of a=20
> 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=20
> 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=20
> achieve the same
> > effect. I figured out to use an intersection with CGOs but=20
> somehow I could
> > not get it to work with a surface definition. May be=20
> somebody else knows how
> > to do this. I'd be interested in it to.
> >=20
> > Here is what I did. Split your scene into their components=20
> and write out the
> > raster3d input files. Remove all headers from the r3d files=20
> and save one
> > header into a control script (master.r3d) If you use vmd=20
> (oops again...) you
> > have to get rid of the object 17 in the surface definition,=20
> otherwise you
> > will not be able change colors, transparency etc. Use=20
> remove_17.pl for this.
> > The animate_bounding.pl script allows you to move the=20
> bounding plane in a
> > given range to find the right orientation. The only way to=20
> do this is by
> > trial and error. A good starting point is a plane defined=20
> by the normal
> > vector 0,0,1 (x,y plane at origin of scene).
> >=20
> > good luck.
> >=20
> >=20
> > Carsten
>=20
>=20
> Dr. Kelley Moremen=20
> 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: mo...@ar...
> (send email with large attachments to: mo...@bm...)
> Website: http://bmbiris.bmb.uga.edu/moremen/lab/
>=20
>=20
>=20
>=20
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>=20