The BioMolViz Project: Difference between revisions

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'''[[:Category:Symmetry/Asymmetry Recognition|Symmetry/Asymmetry Recognition (SA)]]''': A <scene name='85/857774/Sa/1'>(<jmol>
'''[[:Category:Symmetry/Asymmetry Recognition|Symmetry/Asymmetry Recognition (SA)]]''': A <scene name='85/857774/Sa/1'>homodimer of the large kinase Tel1 protein from the bacterium Chaetomium thermophilum</scene> (PDB ID: 6sl0) with each monomer arranged symmetrically around the vertical axis.  A 180 degree rotation <jmol>
   <jmolButton>
   <jmolButton>
     <script>rotate Y 180 50</script>
     <script>rotate Y 180 50</script>
     <text>rotate by 180</text>
     <text>rotate by 180</text>
   </jmolButton>
   </jmolButton>
</jmol>)homodimer of the large kinase Tel1 protein from the bacterium Chaetomium thermophilum</scene> (PDB ID: 6sl0) with each monomer arranged symmetrically around the vertical axis.  A 180 degree rotation around the vertical axis reproduces the initial structure giving the protein C2 symmetry. As an example of an SA1.02 assessment, students would examine a 3D rendering of the structure, coloring the dimer in a way to reveal the symmetry clearly, and show two images to compare the structure as it’s rotated.  
</jmol> around the vertical axis reproduces the initial structure giving the protein C2 symmetry. As an example of an SA1.02 assessment, students would examine a 3D rendering of the structure, coloring the dimer in a way to reveal the symmetry clearly, and show two images to compare the structure as it’s rotated.  


:''SA1.02 Students can rotate a given, rendered molecule and identify axes of symmetry. (Amateur)''
:''SA1.02 Students can rotate a given, rendered molecule and identify axes of symmetry. (Amateur)''
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'''[[:Category:Structural Model Skepticism|Structural Model Skepticism (SK)]]''': The structure shows unacceptably large steric clashes from backbone atoms for the experimentally-determined orientation of three amino acids (Tyr, Thr and Asn) from the <scene name='85/857774/Sk/1'>SK</scene>Streptococcal Protein G in complex with the FC domain of human IgG</scene> (PDB 1D: 1fcc). The viewer should recognize the unfavorable geometry from the displayed clashes and short hydrogen bond lengths. An example assessment for SK2.01 would be to suggest alterations to either main chain or side chain conformations that may alleviate the strain.  
'''[[:Category:Structural Model Skepticism|Structural Model Skepticism (SK)]]''': The structure shows unacceptably large steric clashes from backbone atoms for the experimentally-determined orientation of three amino acids (Tyr, Thr and Asn) from the <scene name='85/857774/Sk/1'>Streptococcal Protein G in complex with the FC domain of human IgG</scene> (PDB 1D: 1fcc). The viewer should recognize the unfavorable geometry from the displayed clashes and short hydrogen bond lengths. An example assessment for SK2.01 would be to suggest alterations to either main chain or side chain conformations that may alleviate the strain.  


:''SK2.01 Students will evaluate a crystal structure for crystal packing effects. (Novice, Amateur, Expert)''
:''SK2.01 Students will evaluate a crystal structure for crystal packing effects. (Novice, Amateur, Expert)''
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