Re: [PyMOL] Visualizing Molecular Orbitals in PyMol

[Martin <mar...@gm...>]

Am Donnerstag, 15. Februar 2007 schrieb BuzB:

> 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
> value.

A good point to start is maybe to look at Learner's APBS plugin. Also there 
should be some documentation about the ?OpenDX? format apbs is using for 
potential maps. It has also isosurface display controls implemented.

> 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?

Sign information? If you're talking about a simple scalar potential, i see no 
problems arise. The probability amplitude should be always positive or what 
do you mean?

> 2. Given a map object, how do I color the mesh depending on the sign
> of the values in the map?

There are 2 things you can do IMHO. Either creating isosurfaces with fixed 
color or color sth else e.g. the sas surface of a protein with the potential 
values.

Cheers
	Martin


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