1. 1 P8 Extra Discussion Slides

2. 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 2

3. Questions 3 1)Why select *H, *I? 2)How to count no. of helices and beta-sheets?

4. Basic amino acid structure 4 http://homepages.ius.edu/GKIRCHNE/peptide.jpg http://www.hcc.mnscu.edu/programs/dept/chem/V.27/amino_acid _structure_2.jpg

5. Labeling of amino acids atoms 5 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)

6. Question 6 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