These hints are numbered to correspond to the questions.

Important: if you don't know where to find parts of Protein Explorer mentioned below, look in the Help/Index/Glossary! You get it by clicking the circled green question mark at the top of the QuickViews page, or there is a link on the FrontDoor page, under "About Protein Explorer". On the FirstView page, click on Protein Explorer © near the top.

1. In FirstView, how many different colors of chains are visible? In QuickViews, how many chains are listed on the SELECT menu? At FirstView, click on backbone trace for more information.
   Click on an "elbow" of each chain and look at the report in the message window to see if it is made of amino acids or nucleotides.
   Optional: Click on the Molecule Information Button, and use the Sequences display to look for chains with identical sequences, and for gaps (rows of dots ...... within a chain). Help linked to the Sequences page gives more information on types of gaps.
   To distinguish DNA from RNA, SELECT Nucleic, and use the link in the middle window.

2. Disulfide bonds are displayed in FirstView. In QuickViews, click FirstView: Reset View.

3. In QuickViews, press the gray button labeled 2^o. Read the help in the middle frame after each operation.

4. In QuickViews, click the button [Ligand] repeatedly to make any ligands disappear and reappear. Read the help in the middle frame to find out how to get full names of ligands. You may also SELECT Ligands, then display and color them as you wish.
   Optional: SELECT Ligand, DISPLAY Contacts. If there is more than one ligand molecule, use SELECT Clicks (one residue per click) to select just one before doing DISPLAY Contacts.

5. (Skip unless you are doing the optional questions.)
   Optional: For active site information, consult the PDB file header (available in the Molecule Information Window). In some cases, there are records for SITE_DESCRIPTION, SITE_IDENTIFIER, and SITE. The latter records list the sequence numbers of critical residues in the site. Use Seq3D (available in the Molecule Information Window) to highlight residues from sequence numbers. You can also use ConSurf (SELECT Evolution) to identify surface patches that are highly conserved during evolution. These are often active sites.

6. SELECT Protein, DISPLAY Spacefill, COLOR Polarity2 (or Polarity3). Use the [Slab] button to view the core. For soluble and insoluble reference proteins, at the FrontDoor, under More Quick-Start Molecules, click on Protein Comparator to see hemoglobin and the potassium channel side by side.

7. SELECT Protein, DISPLAY Spacefill, COLOR Polarity5.
   Optional: Pay attention to the middle frame!

8. (No hints for "surprising or unusual".)

9. To find biological functions, start with the PDB Header (available from the Molecule Information Window). See if your molecule happens to be described in a "Protein Documentary" (search the web for the name of your molecule plus "documentary"). If not, do a general web search for your molecule. Or look it up in a biology or biochemistry textbook.
   Optional: The primary literature reference may also help with the function. It is available (hyperlinked to the abstract at PubMed) on the Structure Explorer link to the Protein Data Bank (available in the Molecule Information Window).

10. (Skip unless you are doing the optional questions.)
    Optional: At the FrontDoor, click (in the middle gray block) on Find your molecule for a list of sites that search the PDB.