This is lecture 16 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers molecular graphics and following a brief introduction is a class discussion of the good and bad features of various molecular graphics programs based on an assignment the class had undertaken. Namely:
Render a PDB structure of protein kinase A in two or more of the following tools: jmol, Pymol, Chimera (UCSF), ICM Browser (MolSoft) and ProteinWorkshop (PDB) (if you prefer another check with me) and in conjunction with a review of the literature highlight the functionally important features on the molecule you have rendered. Submit those renderings highlighting those features as images in your report (10 points). Also report the good and bad features of the tools you used (10 points). Come to class prepared to discuss the good and bad features of the rendering tools you have used.
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