1. How do I get Protein Explorer to work? It won't even show me a molecule! Answer: See Troubleshooting.
2. Can I get Protein Explorer to work with linux? Answer: Yes! See PE with linux.

3. How do I cite Protein Explorer? Answer: See Literature About Protein Explorer.
4. What are people saying about Protein Explorer? Answer: See Literature About Protein Explorer.

5. Where can I get a PDB file for a lipid bilayer? (or NaCl? or cholesterol? or valium? or other molecules not available at the Protein Data Bank?) Answer: Look under the Molecules section at molvisindex.org.

6. How do I use Protein Explorer in my teaching? Answer: See Lesson Plans and Assessment.
7. Protein Explorer is too complicated for my class. Where can I find a basic tutorial in Chime on DNA? (or tRNA? or the ribosome? or an animation of translation? or amino acids? etc. etc.) Answer: Tutorials on over 100 molecules are indexed at molvisindex.org.

8. How do I print a publication-quality image? Answer: See Printing publication-quality images.
9. How do I save
   1. A static molecular image from Protein Explorer for use in Powerpoint, etc.? Answer: See Saving Images.
   2. A rotating molecular image from Protein Explorer for use in Powerpoint, etc.? Answer: See Powerpoint.
   3. The state of Protein Explorer, to resume the session later? Answer: Unfortunately, saving the state is not possible (see Limitations). It is possible to save a script of commands which can be played back later to restore the molecular image. This should be attempted only by advanced users and those willing to spend considerable time at it.

10. How do I mutate the protein? Answer: See mutation.
11. I have the sequence for my protein, but I can't find a PDB file for it. What do I do? Answer: Make sure you've tried both SearchFields and OCA. If there is really no published 3D structure, try homology modeling.
12. How do I make one of those cool presentations using Chime, like the one I've seen on hemoglobin (or DNA, or green fluorescent protein, etc.)? Answer: See Presentations.

13. My question isn't here. What do I do? Answer: Please consult PE's Help/Index/Glossary. If you think your question should be in the FAQ, please tell yours truly.

Feedback to Eric Martz.