Notes and Suggestions

This term, I have a student who’s helping me with designing
educational materials for physical chemistry classes on the university
level. I first had her try out a few commercial alternatives to
Avogadro. We came out on top, but she had some great suggestions.

  • She felt the calculation extensions weren’t organized well. She
    suggested it might be nice to make part of the dialog work like a
    sentence – e.g., “A geometry optimzation will be performed using
    density functional theory…”

  • She liked the builder in Spartan which allows you to pick
    hybridization and shapes for atoms – but didn’t like that Spartan
    forced you to use it. She thought it would be great if Avogadro had a
    tool like that and you could switch from “free-form” to “template” and
    back as needed.

  • Manipulate tool changes. Based on her comments, it was clear that
    she expected to click on a molecular fragment with the manipulate tool
    and move that around. Right now, it defaults to picking an atom. I
    think we should adapt code from the select tool’s "select molecule"
    mode for the manipulate tool.

  • A “best available” force field option, particularly for the “Auto-
    Optimize” tool. The student said that for an "automatic optimization,"
    there were a few too many options. I think it might be nice to have an
    option for the force field which attempts to use MMFF94. If a call to
    OBForceField::Setup fails, then we can fall back to UFF. For most
    cases, this would work really well. (Plus, in the future, if we had
    Amber or CHARMM for biomolecules, that could be used if we found many
    residues in the molecule.)