The BioMolViz Project: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Kristen Procko, Josh Beckham, Jaime Prilusky, Karsten Theis

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 <StructureSection load='2yvk' size='340' side='right' caption='Caption for this structure' scene=''>
-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 prior to inclusion in the repository. These assessments are designed using the Framework. For example, a learning goal within the '''[[:Category:Alternate Renderings|Alternate Renderings (AR)]]''' Overarching Theme is:
+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.
+As an example, a repository contributor might identify the '''[[:Category:Alternate Renderings|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:
+A '''learning objective''' encompassed by this goal is:
 :'''AR1.04:''' Students can infer information from rendering a structure in different ways.
-An '''assessment''' to test if this learning objective has been met would be:
+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.
-To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='86/865933/Zoom_ligand_spacefill/1'>unobscured view of the ligand</scene> 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 <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. 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 <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_-_resi_labeled/1'>active site residues with labels</scene>. Finding polar contacts to nearby residues is generally quite straightforward in most molecular visualization software programs.
+To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='86/865933/Zoom_ligand_spacefill/3'>unobscured view of the ligand</scene> 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 <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. 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 <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_-_resi_labeled/1'>active site residues with labels</scene>. Finding polar contacts to nearby residues is generally quite straightforward in most molecular visualization software programs.
 </StructureSection>
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 [[Category: BioMolViz]]
 [[Category: Alternate Renderings]]
+[[Category: Atomic Geometry]]
 [[Category: Construction and Annotation]]
 [[Category: Ligands and Modifications]]
@@ Line 70: / Line 73: @@
 [[Category: Molecular Interactions]]
 [[Category: Structure‐Function Relationship]]
-[[Category: Topology and Connectivity]]
 [[Category: Symmetry/Asymmetry Recognition]]
 [[Category: Structural Model Skepticism]]
+[[Category: Topology and Connectivity]]