The BioMolViz Project: Difference between revisions

Line 41:

~~One~~ 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 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:

:'''AR1''': Students can create meaningful molecular images to convey features such as secondary structure, CPK coloring, active sites and molecular interactions.

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: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_sticks~~/5'>stick representation</scene>. To view the interacting residues, the learner shows <scene name='86/865933/Zoom_ligand_plus_as_stick/1'>residues within 5Å of the active site</scene>, as sticks and displays them with CPK coloring. 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/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/5'>stick representation</scene>. To view the interacting residues, the learner shows <scene name='86/865933/Zoom_ligand_plus_as_stick/1'>residues within 5Å of the active site</scene>, as sticks and displays them with CPK coloring. Finding polar contacts to nearby residues is generally quite straightforward in most molecular visualization software programs.

</StructureSection>

The BioMolViz Project: Difference between revisions

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@@ Line 41: / Line 41: @@
 <StructureSection load='2yvk' size='340' side='right' caption='Caption for this structure' scene=''>
-One 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 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:
 :'''AR1''': Students can create meaningful molecular images to convey features such as secondary structure, CPK coloring, active sites and molecular interactions.
@@ Line 53: / Line 53: @@
 :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_sticks/5'>stick representation</scene>. To view the interacting residues, the learner shows <scene name='86/865933/Zoom_ligand_plus_as_stick/1'>residues within 5Å of the active site</scene>, as sticks and displays them with CPK coloring. 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/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/5'>stick representation</scene>. To view the interacting residues, the learner shows <scene name='86/865933/Zoom_ligand_plus_as_stick/1'>residues within 5Å of the active site</scene>, as sticks and displays them with CPK coloring. Finding polar contacts to nearby residues is generally quite straightforward in most molecular visualization software programs.
 </StructureSection>