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

[Tim Grüne <grune@embl-grenoble.fr>]

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Hello,
what you could do is to manually delete those residues that make up the
surface that you don't want to display and then recalculate the surface
with GRASP.
Given your problem, this sounds easiest to me. If you still want to show
the other residues, you can use the complete co-ordinate file for those.
It's probably a bit tedious to select the right residues, but you could do
that with a rasmol window next to GRASP window, e.g.

Otherwise: I don't know whether GRASP calculate difference vectors- if so,
you should be able to select those with a certain direction (e.g. negative
z-component), project onto the corresponding residues and use those for
the surface. Just an idea, I haven't tried myself.


I hope I understood your problem correctly.
Good luck,
Tim

--
You don't sew with a fork, so I see no reason to eat with knitting
needles.
		-- Miss Piggy, on eating Chinese Food
--
Tim Gruene, grune@embl-grenoble.fr
EMBL Outstation Grenoble
6 Rue Jules Horowitz
BP 181
F-38042 Grenoble Cedex 9
France


On Tue, 28 Jan 2003 phubbard@post.its.mcw.edu wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> 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.
>
> 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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