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To examine files from PDB, you will need one of the many visualization tools available. I still use Rasmol (available for free and running on many platforms), but there are many other fine tools available. Carol Rohl has a list of several of them on her links web page: http://www.soe.ucsc.edu/~rohl/links.html.
Pick one or more of these tools, get access to a copy, and learn to use it. The programs rasmol, chimera, pymol, Cn3D, and molmol are installed on School of Engineering machines in /projects/compbio/bin/i686, as is Swiss PDB viewer (as deep-view). You should learn how to rotate, zoom, and translate the molecules, how to get different drawings (at least cartoon, wire frame, and space-filling), how to select individual residues, and how to output images in various formats. Most of the molecular graphics programs have home pages with sample images that demonstrate their capabilities.
You can pick up pdb files directly from the PDB web site at http://www.rcsb.org/pdb/, or you can use the pdb-get script in /projects/compbio/bin/ to fetch the file to /projects/compbio/data/pdb/ and return the file name. It is probably worth your time to explore the PDB web site, particularly the search engine, the data uniformity project, various features in beta test, and the molecule of the month.
Pick two proteins of known structure and find something interesting to illustrate in their structure. Write text and make pictures that illustrate your point clearly. Do not take pre-existing images or ones created by a web site, but create your own picture.
Reading several of the "molecule of the month" descriptions on the PDB web site may give you some ideas what to look for in the structures. It could be a static feature, such as an active site or where the protein interacts with another. It could by a dynamic feature, such as a conformation change when binding a ligand (this can often be seen by superimposing structures solved with and without the ligand).
One popular research task these days is to map disease-related SNPs (single nucleotide polymorphisms) onto the structure of the protein that is the gene product, to try to predict how the SNP might disrupt the function.
Another possibility is to superimpose homologous proteins to highlight similarities and differences.
I'm not expecting you to discover anything new about these proteins, but to learn something interesting about them and to make illustrations with accompany text that conveys the story clearly to others. Two informative pictures for a protein are much better than five uninformative ones. A nd don't forget that you'll need explanations to accompany your images.
Hand in this assignment by making a static web page (no plugins needed and working with almost any browser), and sending me the URL. On the School of Engineering machines, you can make web pages by creating files in the .html/ under your home directory and making them publicly readable. JPEG and GIF are the preferred export formats for images on web pages.
The web-page format will limit you to somewhat simpler images than you might use in print, since the resolution is a bit limited. This may actually help you, since there is a tendency toward too much clutter from unnecessary details.
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