Dear Birgit
The MOL2 format will contain partial charge data for each atom, but not the
MEP. Jmol calculates the MEP coloring from the charges.
I am not sure the MEP data can be saved to file. You can save the
isosurface (with the color map, possibly) from Jmol using either "write
isosurface" command or the pop-up menu.
As Otis said, probably there are different methods for calculation in Avogadro
and Jmol for noth the partial charges and the MEP.
Regarding the colors seen, the interval of the rainbow may ve defined as
"absolute" or "relative", or even with user-fixed data as Otis has shown. So
the colors are a convention, no real meaning, you should not worry much
about them.
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