Pim, this is checked in for Jmol 11.3.44. Surprisingly simple.
isosurface CAP [plane definition]
where [plane definition] is one of:
1) {x y z w}
2) any combination of three points (atoms, draw objects, coordinates)
Note that you have to designate the side you want capped. This is done
as follows:
1) {-x -y -z -w} is the other side capped
2) the side capped will be based on a right-hand rule for listing the
three atoms -- going around them with your right hand, in order, thumb
sticks out into space; hand grabs isosurface. So to reverse, just
reverse the order of two of the three points listed.
NOTE:
There could be state problems with this depending upon how the plane is
defined. I'll look into that in time.
In principle one could have any number of these capping planes, but for
now only one.
This works specifically for solvent/molecular surfaces.
Bob
Bob Hanson wrote:
> Interesting! With a tweak or two of the POV-Ray file, you could do
> that today in Jmol --
>
> 1) define the 5 translucent isosurfaces and the molecular structures
> (easy)
> 2) define the sixth isosurface
> 3) use POV-Ray's intersection capability to cap off that one
> isosurface where you see the slab. (trickier)
>
> The main problem I see is that we don't have a way of defining a 3D
> slab in molecular coordinates -- with the perspective the way we have
> done it, it's not obvious how you define a specific slab. But I can
> think of a way or two.
>
> Well, I guess if you first shot it straight on, then in POV-Ray did
> the rotation, that would do the trick.
>
> Yes, that's not a major problem, I think.
>
> Ultimately we might want to have a few POV-Ray-unique commands in Jmol
> to direct something like this.
>
>
> Bob
>
> pim schravendijk wrote:
>
>> Hi Bob!
>>
>> I think anyone would want to do this every now and then:
>>
>> http://skuld.bmsc.washington.edu/raster3d/examples/slice.jpeg
>>
>> This is in raster3D. I guess it means the isosurface would just have
>> to be recreated in such a way that it connects sliced-out parts.
>> Is that possible?
>>
>> --
>> Greetings, Pim
>> http://www.molmod.com
>
>
>
>
--
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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