Glad you like it.
Yes, arbitrary points in space; arbitrary atoms; arbitrary geometric
centers of collections of atoms; arbitrary orientation of ellipsoid;
arbitrary dimensions (provided a=b).
colors/transparency:
The simplest thing to do is to assign an arbitrary id to the isosurface:
isosurface item1 center {1.0 2.0 3.0} ellipsoid {1 0 0 0.5} .....
isosurface item2 center (within(molecule,atomno=3)) scale 5.0 ellipsoid
{1 0 0 0.5} ....
and then refer to that using the $name notation:
color $item1 transparent yellow
color $item2 green
some of this is done in
<http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm>
Bob
Egon Willighagen wrote:
>On Tuesday 27 June 2006 21:16, Dan Gezelter wrote:
>
>
>>>http://www.stolaf.edu/people/hansonr/jmol/test/proto and let me
>>>know if
>>>what I have done there in relation to ellipsoids is sufficient for
>>>you.
>>>The basic format is:
>>>
>>> isosurface center {x y z} ellipsoid {cx cy cz f_ab}
>>>
>>>or
>>>
>>> isosurface center (some_atom_expression) ellipsoid {cx cy cz f_ab}
>>>
>>>
>>Oooooo..... Ahhhhhhhhhhhh.....
>>
>>Very cool!
>>
>>
>
>Do I understand correctly that this also works on arbitrary points {x y z} in
>space?
>
>This would mean that Jmol can now render pharmacophores!
>
>Oooo.... Ahhhh.... very cool, indeed!
>
>How can a set color and transparency?
>
>Egon
>
>
>
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