Warren,
Can PyMol actually write raster3D objects? That's news to me. I did a
couple of the clipped, bounded surfaces in raster3d since it supports it
supports the option and was easier to implement than in PovRay. Again
the biggest drag is always to find the right orientation of the clipping
planes. If we can achieve this in PyMol then the rest is fairly easy.
Cheers,
Carsten
> -----Original Message-----
> From: Warren DeLano [mailto:war...@delsci.com]
> Sent: Friday, May 01, 2009 8:53 PM
> To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] object-specific Z-clipping
>
> Carsten,
>
> I think you're on to something.
>
> So long as this rendering problem remains too hard for us to solve
with
> PyMOL alone, probably the next best thing would be for us to figure
out
> at least an interim PovRay or Raster3D-based process for creating such
> figures. Having an object-selective but non-renderable OpenGL-based
> clipping plane available could certainly help with that!
>
> Cheers,
> Warren
>
> > -----Original Message-----
> > From: Schubert, Carsten [PRDUS] [mailto:cschu...@its.jnj.com]
> > Sent: Thursday, April 30, 2009 1:40 PM
> > To: Warren DeLano; pymol-users@lists.sourceforge.net
> > Subject: Re: [PyMOL] object-specific Z-clipping
> >
> > Hi Warren,
> >
> > I would be interested to see the OpenGL version implemented,
> > despite the lack of raytracing support. In a pinch the draw
> > command could just be sufficient to produce a good picture.
> >
> > As for the implementation in a raytracer context I second
> > Tsjerk's and Harry's thoughts on the subject. Probably some
> > sort of PovRay based implementation would help in the
> > interim. What I find most challenging with that approach is
> > the fact that the placement of the clipping objects is
> > difficult to achieve in PovRay since it lacks the
> > interactivity of a graphics program. I.e. finding the right
> > cut through a protein surface when depicting a ligand in a
> > cut-away surface is tough. Although there are other ways to
> > achieve this they require some "cheating" or creative use of
> > Photoshop/PowerPoint to phrase it differently.
> > I am thinking that if it would be possible to write out the
> > orientation of the clipping planes/slabs as PovRay objects,
> > they could be used as bounding objects in PovRay. Since the
> > placement of the clipping planes is easily achieved in Pymol
> > this could be done interactively. All the user has to do is
> > to associate clipping plane(s) with a graphics object, place
> > the planes and write out the corresponding PovRay code of the
> > object and the planes. Of course the code of the clipping
> > objects needs to be separate from the other stuff, so
> > expanding the "PovRay tuple"
> > into (matrix,clipping,data) parts would help.
> > Getting it all together requires some knowledge of PovRay but
> > examples in the Wiki should help to get over the initial pain.
> >
> > Any thoughts on this approach?
> >
> > Carsten
> >
> >
> > > -----Original Message-----
> > > From: Warren DeLano [mailto:war...@delsci.com]
> > > Sent: Wednesday, April 29, 2009 10:36 PM
> > > To: Mankin Alexander; pymol-users@lists.sourceforge.net
> > > Subject: Re: [PyMOL] object-specific Z-clipping
> > >
> > > Sorry, still not done (I have made two attempts, but both failed).
> > >
> > > While OpenGL supports arbitrary clipping planes, accomplishing
this
> > > correctly in the ray tracer is a much harder problem that one
might
> > > think...
> > >
> > > Cheers,
> > > Warren
> > >
> > > > -----Original Message-----
> > > > From: Mankin Alexander [mailto:sh...@uic.edu]
> > > > Sent: Wednesday, April 29, 2009 6:18 AM
> > > > To: pymol-users@lists.sourceforge.net
> > > > Subject: [PyMOL] object-specific Z-clipping
> > > >
> > > > Dear all,
> > > > Does anyone know whether object-selective z-clipping has been
> > > > implemented in the newer Pymol version(s)? If not, has
> > anyone found
> > > > any solution around (since 2002 no new threads on the matter)?
> > > > Thanks,
> > > > Shura Mankin
> > > >
> > >
> > >
> > >
> > >
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