Joost -- I'm forwarding this answer to the list, because I think others
might be interested in it. You write:
It would be nice to be able to slap per frame or only one frame instead
of all frames at once. This allows you to se a internal pocket of a
protein by hiding the front ...% of the protein but showing the entire
ligand at the same time.
That is an intriguing idea. I think you can do it already, actually.
There are two types of slab and also two additional methods:
The original Chime sort: You define a percent from front to back; the
renderer throws out pixels that are not in range. As the model is
rotated, different parts move into and out of range. This would probably
be just too strange if done on a per-model basis. It would not be
impossible to implement, though.
A new "internal" sort introduced in Jmol 11.1.5. In this mode you define
the slabbing plane, and the parts of the model on one side of this plane
are removed. I think this is more like what you are thinking of -- where
one part of the model is "cut away", and as the model is rotated, the
slabbing plane rotates with the model.
slab plane x=3; slab on
slab plane {1 0 1 0}; slab on
slab hkl {1/2 1/2 1/2}; slab on
A new manual slabbing capability introduced in Jmol 10.9.71. You can set
the Chime sort of slab and then select atoms that are "clickable" or
not. Only atoms currently in range are clickable. So this allows you to
programmatically do things with atoms based on their current orientation
of the model.
slab 60; slab on;refresh;display clickable;slab off;
# now the slab appears to be fixed as the model rotates
A new select "within" criteria introduced in Jmol 11.1.12 allows you to
select atoms directly depending upon their relationship to a specified
molecular coordinate plane.
display 1.1 and within (-999, plane {1 0 1 0}) or 2.1
So I would encourage you to check these methods out and see if any do
what you are envisioning. I think all are described in the documentation.
--Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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