I have been struggling to get Avogadro 1.1.0 to read .molden files for MO surfaces. Having played about with the input structure of the molden files i've identified 3 issues:
1) Avogadro requires a blank line before and after each line of the ATOMS section. Otherwise only 1 atom is displayed. This is not standard in the .molden file format so seems like a bug in the avogadro/openbabel parser?
2) MOLPRO specific issue: Molpro makes .molden files where the exponents of the GTOs are in the form x.xxxxxD+yy or x.xxxxxD-yy, where the standard is for x.xxxxxE+yy or x.xxxxxE-yy. The change from E to D for exponent is apparently not supported by Avogadro/Openbabel and causes any orbital render to crash. Manually changing the .molden file works around this but is a pain!
3) Avogadro crashes when trying to render core MOs with very small sizes if the ISOvalue is set too high. By reducing the ISO you can render these orbitals ok, but it seems that there is a crash if the rendering produces only zero values or something similar. This is general to all .molden renders, perhaps also to .fchk ones? - i haven't tried.
4) Orbital energies and occupation numbers are not read out of the .molden file into the orbital rendering list window.
Attached is an avogad.molden file from molpro for water (HF/6-31g) (modified to make exponents as E+ or E- and to add blank lines in the ATOMS section). This works around issues 1 and 2, but not 3 or 4, so you can at least render the orbitals. The original from molpro is molpro.molden for comparison.
Thanks for all your hard work making Avogadro for free, it's massively appreciated..