I'm trying to develop a way to display quantum mechanical molecular
orbitals in PyMol.
I can compute the probability amplitude at all points in space around
a molecule; at the moment I'm using an extended h=FCckel program to do
this. I would like to be able to draw a mesh or a surface, that
represents a surface of constant probability amplitude, and color the
mesh or surface depending on the sign of the probability amplitude.
For instance, the contour would still be displayed if the probability
amplitude at a particular surface was 0.1 or -0.1, but would be
colored blue for positive, and red for negative.
I think a way to do this would be to generate a map, like an electron
density map, and then generate a mesh from this, contoured at a given
To do this I would like some help;
1. Given that I know the probability amplitude at all points in a
given volume of space, how do I generate a map? Will having sign
information complicate matters?
2. Given a map object, how do I color the mesh depending on the sign
of the values in the map?
Thank you very much! and all the best,