The BioMolViz Project: Difference between revisions
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== Framework Overarching Themes == | == Framework Overarching Themes == | ||
<StructureSection load='' size='450' side='right' caption='One of the 12 overarching themes is MI, molecular interactions, illustrated here by the lambda repressor bound to the major grooves of double-stranded DNA' scene='85/857774/Molecularinteraction/1'> | |||
The twelve overarching themes of the Framework are outlined below, and the associated learning goals and objectives, can be viewed on the [https://biomolviz.org/framework/ BioMolViz website]. | The twelve overarching themes of the Framework are outlined below, and the associated learning goals and objectives, can be viewed on the [https://biomolviz.org/framework/ BioMolViz website]. | ||
'''[[:Category:Atomic Geometry|Atomic Geometry (AG)]]''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes. | '''[[:Category:Atomic Geometry|Atomic Geometry (AG)]]''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes. As an example, <scene name='85/857774/Glucose/1'>a ring form of D-glucose (ß-D-glucopyanose) </scene> is shown. A C-O-C bond angle in the sugar ring is shown, in addition to the dihedral/torsion angle of the center bond defined by four consecutive ring atoms (C-C-C-O). Viewers should be able to differentiate bond angles from dihedral/torsion angles and predict changes from ideal angles. An example assessment that encompasses objectives AG1.02, AG1.03, and AG1.04 would require students to measure the C-O-C bond angle, recognize that the ideal tetrahedral bond angle geometry is 109.5º and describe this deviation due to the chair conformation of the structure. An assessment that encompasses AG3.03 would require students to display and describe the atoms involved in measuring the dihedral angle. | ||
'''[[:Category:Alternate Renderings|Alternate Renderings (AR)]]''' ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling. | '''[[:Category:Alternate Renderings|Alternate Renderings (AR)]]''' ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling. | ||
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'''[[:Category:Topology and Connectivity|Topology and Connectivity (TC)]]''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering. | '''[[:Category:Topology and Connectivity|Topology and Connectivity (TC)]]''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering. | ||
</StructureSection> | |||
== References == | == References == | ||
