1 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.

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Presentation transcript:

1 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 2

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

Basic amino acid structure _structure_2.jpg

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)

Question 6 Hydrogen is usually not shown in PDB structures, unless the structure is of high-resolution (less than 1 Angstrom)