[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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         ***

> > 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.

  This is an excellent idea. Even if the molecule isn't planar its
curvature might be approximated by two, three or four (flat) clipping

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

  Don't know about POVSCRIPT either but POVRAY allows you to clip objects
with any other object of any shape and size.

object { my_object my_textures clipped_by { my_complex_clipping_object }}

or what I prefer for some technical reasons:

intersection {

   object { my_object .... }
   object { my_complex_clipping_object }