Re: [Jmol-developers] ellipsoids and isosurfaces

[Bob H. <ha...@st...>]

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
>
>  
>