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RE: [o-info] RE: [ccp4bb]: Generating surface figures pt. II
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Yes, it is possible that you could pull this off in PyMOL, but it wouldn't necessarily be easy.
Essentially what you'd need to do is only "show surface" for atoms on the far side of the pocket. Atoms on the near side will still be present in the calculation, but their surfaces will not be shown.
Unfortunately, the surface will have a jagged quality to it even after setting surface_quality=1
It seems to me that we need some better tools for specifying exactly which part of a protein surface is shown (pocket vs surface, concave vs. convex, etc.), so please direct brainstorms my way if you have any good ideas about how to do this. The geometry is easy, it's the proposed user interface that's difficult.
Warren L. DeLano, Ph.D.
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
From: Schubert, Carsten [mailto:Carsten.Schubert@3dp.com]
Sent: Tuesday, January 28, 2003 10:07 AM
To: 'Tim Grüne'; firstname.lastname@example.org
Cc: email@example.com; firstname.lastname@example.org
Subject: [o-info] RE: [ccp4bb]: Generating surface figures pt. II
Actually I think that may not work. Grasp may just calculate a closed surface on the subset of present residues.
In GRASP you could scribe the surface to get rid of all unwanted residues and try to render or export and render. Alternatively you may want to look into clipping and bounding planes in Raster3D, which allow for cut-away surfaces, although the learning curve is a bit rough.
Pymol has an annoying (and valuable once you got to know it) side-effect on generation of a surface from a subset of atoms. It will generate an open surface only around selected residues. The edges look a bit rough but I believe there is a parameter to adjust the grid of the produced surface to smooth things out.
> -----Original Message-----
> From: Tim Grüne [mailto:email@example.com]
> Sent: Tuesday, January 28, 2003 12:13
> To: firstname.lastname@example.org
> Cc: email@example.com; firstname.lastname@example.org
> Subject: Re: [ccp4bb]: Generating surface figures pt. II
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
> 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,
> You don't sew with a fork, so I see no reason to eat with knitting
> -- Miss Piggy, on eating Chinese Food
> Tim Gruene, email@example.com
> EMBL Outstation Grenoble
> 6 Rue Jules Horowitz
> BP 181
> F-38042 Grenoble Cedex 9
> On Tue, 28 Jan 2003 firstname.lastname@example.org 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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