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P8 Extra Discussion Slides

Visualization of 3-D structure

• PyMOL is a tool/software that helps with the visualization of 3D structure

• PyMOL does not help with the modeling of 3D structure (primary sequence 3D structure; you will learn modeling in practical 9)

• Other software that help with visualization of 3D structure: MolMol, SoftMol, Protein Explorer, Rastop, Rasmol

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Questions

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1) Why select *H, *I?

2) How to count no. of helices and beta-sheets?

Basic amino acid structure

4http://homepages.ius.edu/GKIRCHNE/peptide.jpg

http://www.hcc.mnscu.edu/programs/dept/chem/V.27/amino_acid_structure_2.jpg

Labeling of amino acids atoms

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• Color scheme: Red=Oxygen; Gray=Carbon; Blue=Nitrogen; Cyan=Hydrogen; Yellow=Sulphur

• A for alpha, B for beta, G for gamma, D for delta, E for epsilon, Z for zeta, and H for eta

Hydrogen is usually not shown in PDB structures, unless the structure is of high-resolution (less than 1Angstrom)

Question

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Hydrogen is usually not shown in PDB structures, unless the structure is of high-resolution (less than 1 Angstrom)

http://www.hcc.mnscu.edu/programs/dept/chem/V.27/amino_acid_structure_2.jpg