From: John Stone (
Date: Wed Nov 23 2011 - 09:22:43 CST

  You can use spatial atom selections to do much the same thing as a
user-defined clipping plane, but removing entire atoms and not just
clipping their drawn geometry. The syntax for making such atom selections
is described in the VMD User's Guide, but here are a few examples of
simple spatial atom selections, some of which combine math functions:
  "z > 0"
  "not water and x > 0"
  "sqrt(x*x + y*y + z*z) < 30"
  "protein and ((z > 0 and (x/z < -0.5)) or z < 20)"

  John Stone

On Wed, Nov 23, 2011 at 02:48:33AM -0800, Philippe Bopp / temporary wrote:
> Hi all,
> a day's worth of googling could not solve this one:
> I would like to clip a representation in VdW (and/or) CPK
> without the black spots that (it seems to me) occur when
> a sphere is cut by a clip plane (see attached). In other
> words, I would  like the VdW/CPK-atom to be removed as
> soon as any part of its sphere is cut by a clip plane, not only
> when the center is above/below the plane.
> I could also live with something like an atomselect that
> refers to the clip  plane, but could not find that
> either. A piece of tcl code (at which I am not good at all)
> would also be welcome.
> thanks
> Philippe
> -----------------
> Philippe A. Bopp
> philippebopp AT       (private)
> Philippe.Bopp AT (office)
> -----------------

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