Those teaching and performing research in the molecular sciences, especially chemistry and biochemistry, are aware of the need for both students and practitioners to possess a kind of "literacy" which is based on multiple dimensions, both spatial and temporal. It is difficult to define precisely what skills one must possess before one can be considered literate in this manner, but it is important to do so from a pedagogical point of view. Below is a list generated from the brainstorming of a small number of scientists. I submit this list to the chemistry & biochemistry community for feedback. Please send me your comments on the list below as well as new items which you feel should be included. I will update the list regularly and eventually publish the results.
Robert Bateman
robert dot bateman at usm dot edu
Specifically, students exposed to molecular visualization should be able to:
1. Recognize tetrahedral vs. planar geometries around C atoms, and understand
and measure dihedral angles
2. Recognize the common metal geometries
3. Gain an approximate sense for the atom sizes and contacts in a stick or ribbon
figure and for the connectivities in a space-filling figure
4. recognize and analyze chiral or "handed" structures including chiral
carbons and asymmetric higher order structures such as helices
5. recognize and analyze symmetric structures such as meso compounds and axes
of rotational symmetry in macromolecules.
6. locate the covalent and the hydrogen bonding interactions within and between
molecules
7. identify electrostatic, H-bond, and buried surface interactions binding macromolecular
assemblies together
8. identify key components and 3D relationships in an enzyme active site that
underlie its specific catalytic chemistry
9. make reasonable predictions about the effect of a specific mutation on the
structure or function of a molecule
10. when watching the conformational movements of macromolecules, identify what
moves and how
11. recognize similarities between or within protein folds
12. follow the path of a biopolymer chain through the molecule (topology) and
describe or diagram its major features
13. extract the intended information and relationships from structural figures
in papers and slides in seminars
14. download and visualize 3D coordinates relevant to a paper, to understand
or check out its structure-based claims
15. construct a graphical representation that effectively communicates a 3D
concept of their own to others.
Students who have mastered these should be able to explore in 3-D the overall molecular organization of macromolecules such as proteins and nucleic acids, grasp the structural details that underlie that organization, and ferret out the critical relationships at binding and active sites.