PDB_coords

PDB_coords - yields 932(Note This was a search on 4 Oct...

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February 21, 2007 Getting Coordinates from the Protein Data Bank Chem 391 The Protein Data Bank (PDB) is a repository of 41,814 macromolecular coordinates (as of 20 Feb 2007) run by the Research Collaboratory for Structural Bioinformatics (RCSB). Most of the coordinates are of proteins. However, there are structures of nucleic acids and carbohydrates, too. To retrieve coordinates from the PDB: 1. Open a web browser. 2. Point your web browser to www.pdb.org to bring up the Protein Data Bank home page 3. In the search box, enter the PDB ID (a unique set of four alpha-numeric characters that specify each database entry, it is usually found in the published paper), the name of the macromolecule, an author's name, or other information. 4. PDB retrieves a list of all entries that match your input. For example, searching for “carboxypeptidase” might yield 154 structures, for “myoglobin” yields 228, and for “lysozyme”
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Unformatted text preview: yields 932. (Note: This was a search on 4 Oct 2005 using the "Full Text Search" option.) 5. Your search may yield multiple entries. If so, scroll through the list of results to find the specific macromolecule you want to download. 6. Click the desired PDB ID code or the EXPLORE button. 7. To view the structure, click the "View Structure" link. PDB allows you to view the structure in a variety of different forms. For example, the QuickPDB button posts a basic drawing within the web browser. RasMol is a freeware program that allows you to view PDB coordinates in 3D. The web page has links for downloading RasMol, if it’s not already on your system. 8. Click "Download/Display File" to save PDB file to disk. 9. Once downloaded you may use Cn3D, RasMol, Chimera, or other program to view the coordinates....
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