I think what you want is to generate the electrostatic potential mapped onto the molecular surface (i.e, the van der Waals surface).
In version 1.x, do this:
- Set the surface type to Van der Waals
- Set the “color by” to Electrostatic Potential (this will use Gasteiger charges)
- Change the resolution if you wish
That’s it. You’re right that at the moment, this is not possible in Avogadro 2 (beta).
