Exercise 10

{A. Insight II on an SGI Computer}

{1. Logon to an SGI computer and activate Netscape Communicator}

{2. Activate Insight II}

{3. Insight II documentation}

{B. The Insight II tutorial "Getting Started with Insight II"}

{1. Activate the Insight II tutorial "Getting Started with Insight II"}

{2. Do the Insight II tutorial}

{a. The "cheaters" way of doing the Tutorial}

{b. A "better" way of doing the Tutorial}

{c. The first Three Pages of Commands in the Tutorial: use of Lysozyme}

{d. Include comments in your Notebook}

{e. Answer the Questions as you proceed through the Tutorial}

{C. Questions: }

1. What is Insight II and what does it do?
2. What are the modules in the Insight II package, and what do each do?
3. What are 4 additional applications in the MSI package, and what does each do?
4. How does one use the mouse to translate and rotate a protein model?
5. How are rotations in each of the three dimensions (about x,y,z axes) correlated with motion of the mouse?
6. In what three different ways does one make choices using the pulldown menus?
7. What is the comparable way of making choices using the command line?
8. What is the function of the Temperature Spectrum?
9. What happends to the cylinders and ribbons when you rotate the molecule?  why is this?
10. How are hydrogen atoms represented in Insight II?
11. What is a subset of atoms and how are such used in Insight II?
12. How is the subset called ACTIVE_SITE used in the tutorial?
13.  What are the three numbers used to choose a "color" in Insight II such as used in the color for the active_site atom subset?
14. What "Molecular_Spec" was used in the "Create Surface" operation for the Active Site, and why?
15. Why does the solid surface become a series of dots when the molecule is rotated?
16. What are the four steps in displaying the electrostatic potential in color of the active site surface?  Include the purpose of each step in your answer.
17. Why are the colors of the surface then adjusted?
18. Comment on the logic of the steps in building small docking molecules.
19. What is the substrate of Lysozyme, and how does the molecule you constructed mimic this substrate?
20. Based on this substrate, why do you think tears from eyes are a good source of lysozyme?
21. What does the energy minimization step in the Discover module do?