Hints for Discovery in Protein Explorer
Revised Sept. 2004.
These hints are numbered to correspond to the
shorter list of 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 every
(except FirstView, where it is near the bottom).
There is also a link on the FrontDoor page, under
"About Protein Explorer" (right-most gray column).
- 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.
- Disulfide bonds are displayed in FirstView. (To get back to FirstView,
open the PE Site Map, from which Reset Session.)
- In either Features of the Molecule or
QuickViews, press the gray button labeled
2o. (When in QuickViews, read the help
in the middle frame after each operation.)
- At Features of the Molecule, a section near the bottom
of the control panel (scroll down) lists all ligands, including their
full names. You can click on each one to locate where it is in the
- SELECT Protein, DISPLAY Spacefill,
Use the [Slab] button to view the core.
SELECT Protein, DISPLAY Spacefill, COLOR Polarity5.
- (No hints for "interesting, surprising or unusual".)
- To find biological functions, first look at
PE's Features of the Molecule
As another strategy, 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.
- Use the link to the PE Site Map (on every control panel in PE)
to access External Resources. There, go to Probable Quaternary