Re: [ccp4bb]: Generating surface figures pt. II

[Ethan Merritt <merritt@u.washington.edu>]

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On Tuesday 28 January 2003 07:35, phubbard@post.its.mcw.edu wrote:
>
> Thanks for the replies; however, I may not have phrased the question
> very well. I'll use an analogy -
>
> I have a GRASP surface file which covers the region of protein which
> is within 5A of the ligand (i.e., the ligand binding pocket). This
> pocket looks like a sock - ankle part on the surface and toes in the
> core of the protein. I have played round with the transparency
> setting of this sock in POVSCRIPT, but it doesn't make things clear.
> What I'd like to do is cut the front part of the sock out, so only
> the back part of the sock can be seen (i.e., the part of the surface
> which is normally hidden). Since the ligand isn't flat I can't just
> slab through. I need a non-planar plane to cut out the front of the
> surface.

I don't understand why a bounding plane won't do, so long as it
only affects the surface itself.  This is easy to do in Raster3D -
just attach a bounding plane to the surface.  If you really need to
also slice based on multiple, intersecting, planes that also is possible,
although I have not written up separate instructions.  You could look
at the ORTEP-like output mode for slicing an octant out of an atomic
surface, as used by rastep. 

I don't know if there is a similar option in POVSCRIPT, but POVRAY
itself must surely support similar bounding surfaces?




>
> Hope that's more clear.
>
> Thanks for your help
>
> AGS
>
> > Hi add,
> >
> > Another non-CCP4/non-O question for you. Does anyone know how to
> > generate a figure where only the hidden part of the surface is
> > displayed?
> >
> > I have a GRASP surface file covering a ligand binding cavity, and
> > would like to show it overlayed with the ligand. So would like to
> > just show the hidden part of the surface (tantamount to a
> > Z-slice/slab, but not since the plane is not flat)
> >
> > I have been using POVSCRIPT/POVRAY.
> >
> > Thanks
> >
> > AGS
> >
> >
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-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002