Re: [Jmol-developers] Initial .cube file isosurface support

[Miguel <mi...@jm...>]

> On a small aside: you seem to consider a molecular orbital with a
> negative cutoff as a different orbital than one with a positive cutoff.=


Yes, I understand

> Chemists don't see it that way since what really has physical
> significance is the square of the orbitals, so the negative isosurface
> and the positive isosurface are considered at the same time. The reason=

> to use signs is that the molecular orbital value can be negative, so
> the mathematical construct does have that feature. The main reason, I
> think, is that it is easier to see where nodal planes are, i.e, places
> where the MO value goes through zero, which also makes it easier to see=

> what the symmetry of the orbital is.

The problem is ... I think that you want to be able to color the positive=

and negative orbitals differently.

I thought that this was the best scheme to be able to give control over
color and display attributes of each independently.


>> Q: Are you saying that a particular surface should be tied to a
>> specific
>> 'model' ?
>
> Yes indeed.

This would solve your 'animation' problem too ... I'll think about this.


Miguel