The BioMolViz Project: Difference between revisions
No edit summary |
No edit summary |
||
| 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. | :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/ | 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. | ||
</StructureSection> | </StructureSection> | ||
| Line 59: | Line 59: | ||
<references/> | <references/> | ||
Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7. | Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7. | ||
Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991. | Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991. | ||