How do I find pdb files to display with Chime?

The easiest way to start a Chime page is to find a pdb file off the internet.  Okanagan University College has a large collection of files, cross indexed by name, structure, function and formula.  If you can't find what you are looking for there, you can search the Internet with a search engine, such as Alta Vista.  Searching for aspartame pdb produces many web sites which have a Chime image of aspartame (a.k.a. Nutra Sweet).  The National Institutes of Health also has links to PDB Databases, which are particularly useful if you are looking for macromolecules, such as proteins and DNA. 

Once you have found a page that displays the molecule you want, right-click* on the molecule to activate the Chime menu.  Pick the File - Save Molecule As... option, set the dialog box to save the file on the N: driveand press the save button.  You may change the file name if you wish, but don't change the extension.  To see your molecule, click on the File command from the browser menu bar.  Pick the Open Page option and press the Choose File... button.  Set the dialog box to look at all file types on the A: drive and open your pdb file.  The image may look different because it will be displayed with the default parameters.  Later we will learn how to customize the image. 

On the next page we will learn how do create our own mol files, if the one you need is not available on-line.

* click and hold on a Mac

Aspartame (a.k.a. Nutrisweet)

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