How to Find Your Favorite Protein (YFP) to be viewed by Jmol

This is a part of an assignment for Molecular Biology or Immunology at Davidson College.

To find a Jmol image, go to this web site: Protein Data Bank (PDB), an international repository for all protein structure. From this page, you can search by key words or PDB ID number (if you know it).

If your query is successful, you will get at least one hit. Click on the entry about which you want to learn more. You can view the structure before downloading it using the menu option to the left. Or you can download it immediately following the download link. You can also learn more about the protein by getting the cited papers associated with this structure.

Once you are ready to download, choose the option (X) that says "PDB" and no compression. You will want to save this file on a hard drive locally. Now you can upload this file to the BioWeb server. Unfortunately, Jmol does not allow you to view the local copy of the file, but you can view it at PDB before you download the file.

When you are ready, you can post this file on the BioServer using an FTP program like Fetch or CuteFTP. Go to the Jmol Help page to find out how to insert a .pdb file into your html file.

See a list of molecules used for various biology courses.

Learn How to search for the sequence of YFP.

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