homework_onufriev - within the PDB file • Make a cartoons...

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Assignment 0 (warm-up) In this assignment you will work on a simple warm-up exercise in structural biology. Please provide TYPED solutions, no more than three pages long, including pictures. When done, just bring the print- out to class. Go to www.rcsb.org/pdb , find and download any protein whose name starts with the same letter as your last name. To get to the PDB record itself click EXPLORE . At the Download/Display File window choose complete with coordinates and TEXT . Ideal protein size for this exercise is 100-300 residues. Consider only ones that are produced by X-ray: search for something like X-RAY DIFFRACTION
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Unformatted text preview: within the PDB file. • Make a cartoons or ribbons picture of your protein using something like rasmol , pymol , VMD , or any other structure vi-sualization package. (most can be easily installed on any platform, including your laptop. Links to many of them are available on the PDB site). Attach the picture to your report. • Find out what the Ramachandran Plot is and generate one for your protein. Attach to your report. • Are there any alpha-helices in your protein? • Very roughly, what percentage of residues in your protein is in alpha-helical conformation?...
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