The broader goal of the BioMolViz project is to build a repository of assessments that instructors can use in their courses to evaluate visual literacy gains. These assessments are written in teams, peer reviewed, and will undergo validation by an expert panel. Using the Framework, these assessments are designed from the learning objectives. The twelve overarching themes of the BioMolviz Framework, and the associated learning goals and objectives, can be viewed on the BioMolViz website.
As an example, a repository contributor might identify the Alternate Renderings (AR) Overarching Theme as an area they wish to target with their assessment. One learning goal within the AR theme is:
- AR1: Students can create meaningful molecular images to convey features such as secondary structure, CPK coloring, active sites and molecular interactions.
A learning objective encompassed by this goal is:
- AR1.04: Students can infer information from rendering a structure in different ways.
An assessment that can be used test if this learning objective has been met can explore protein-ligand interactions. An example of how this assessment may be described to the learner is provided below.
- Given the structure of 5-methylthioribose 1-phosphate(MTRu-1-P) isomerase bound to MTRu-1-P (PDB ID: 2yvk chain A), use Jmol (or another molecular visualization tool such as Chimera or PyMOL) to identify the amino acids in the protein that interact with the ligand.
Example Assessment Solution
Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process
To show mastery, the learner will first focus on subunit A of the complex, hiding subunit B for clarity. An unobscured view of the ligand is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a stick representation. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site as sticks and displays them with CPK coloring. For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can hide the cartoon rendering of the protein, and then show the active site residues with labels. The learner then executes a command to show hydrogen bonds within the active site, including those to the ligand, or measures polar contacts manually.
