| Gribskov & Smith |
BIMM 141 Laboratory |
Spring 2001 |
Introduction to Bioinformatics
This exercise focuses on the use of Silicon Graphics (SGI) Unix computers for protein 3D operations such as modeling, threading, docking of small molecules, interactions with DNA, and so on. SGI computers are renowned for their high level graphics capabilities and have long been the computer of choice for these types of operations.
The main activity of this Exercise is execution of the primary tutorial for Insight II
Insight II is one of several excellent protein 3D computer programs that are commercially available. Insight II is a very robust set of programs capable of doing most computer operations involving 3-dimensional manipulations of proteins, including modeling, threading, docking of small molecules, interactions with DNA, energy minimization, and so on. Perhaps because of its extenisve capabilities, learning how to use Insight II easily and efficiently takes some time.
Insight II comes with an extensive set of Tutorials. In this Exercise, we will just do one of the Tutorials, the basic one called "Getting Started with Insight II".
We first get set up on an SGI computer to do the Exercise and to run Insight II.
{1. Logon to an SGI computer and activate Netscape Communicator}
Logon to an SGI computer and turn on Netscape Communicator
in the usual way.
Go to BIMM 140
home and Exercise
10
Do Exercise 10 in the usual way by using the Exercise 10 Template
and Netscape Composer.
First get going with InsightII on your SGI:
a. In the first Netscape window (ACS help), go to "Setup
and starting Insight II"
b. Do in a Console window at the prompt: prep
insight
c. Then do at the prompt: insightII
Note: typical of Unix, these are case-sensitive commands !!!
This will bring up InsightII ...
You have access to InsightII documentation available on the
Web at ACS;
In a Netscape window, bring up the URL: file:/software/nonrdist/msi/2000/doc/index.html
click on Insight II 2000 ... and then click on "Insight II"
...
This will bring up the rather extensive and complete documentation
...
Examine some of this documentation and comment in your Notebook.
We next do the basic Insight II tutorial "Getting Started
with Insight II" .
This is the main activity of Exercise I0.
Answer the Questions below as you proceed through the tutorial.
{1. Activate the Insight II tutorial "Getting Started with Insight II"}
Do either of the following:
1) click on the "Pilot" button (the one on the left
with a graduation hat)
2) click on the "Help" pulldown menu and choose
"Pilot_Tutorials"
Choose "Select this to see a list of the available Online
tutorials"
Then choose "Insight II" tutorials
Note the large number of Tutorials available and what their topics
are ...
Then choose "Application 1 - Getting Started with Insight
II"
Both of these methods bring up the "Pilot" version of
the tutorial ...
{2. Do the Insight II tutorial}
Do the "Getting Started with Insight II" Tutorial,
answering Questions below as you go along ...
To do any of these Tutorials, you proceed through each of the
Insight II commands given in the Tutorial.
Insight II performs each step of a given task via execution of
these commands.
The commands can be executed in one of two main ways:
1) type in the command on the command line below the black, graphic
window in the Insight II screen display.
2) use the PullDown Menus and Icon choices in the left Icon Display,
to make appropriate choices of commands and options within each
command.
The Tutorials permit the User to do both of these in execution of each command in the tutorial.
The command associated with each window in a Tutorial is shown, one after the other, at the bottom of the Tutorial window, as well as near the top of the window.
{a. The "cheaters" way of
doing the Tutorial}
If you click on the solid green right-pointing single
arrow head near the top left of the Tutorial window, the command
shown will be executed !!
Thus, you can "cheat" and just go through the tutorial
without learning anything just by repeated clicking of this button
...
However ... this "cheating" option doesn't always
work anyway, since some of the commands do not appear to be set
up completely syntactically correctly ... !?!?!
Further, one of the green arrow buttons will even automatically go through the whole tutorial for you, step by step, assuming that there are not many errors in the written commands !!
{b. A "better" way of doing the Tutorial}
Read the material in any given Tutorial window to see what
you are doing.
Then read the command at the bottom to see what commands
and options are used to actually do this.
This execute the command by choosing options in the Pulldown Menus and left panel Icons.
This will take a little ingenuity on your part, but is the way to actually learn how to use Insight II.
For example, if a command is to Create a Molecule, you go to the "Molecule" pull-down menu and then choose "Create" ... so the steps in a command appear sometimes to be reversed ...
Steps in a command with a minus sign are generally options you are NOT supposed to choose ...
You thus in this way execute a complete command by doing sequentially
three types of operations:
1) select items from Pulldown Menus or Icon Buttons
2) click on options within menus, to select such or deselect such
3) type in names of molecules, atoms, files, etc in appropriate
Text Windows
These operations for a given command in the Tutorial mimic very closely the command as written out in the Tutorial window ...
Thus, you learn Insight II by actually doing the operations involved in a variety of commands ...
{c. The first Three Pages of Commands in the Tutorial: use of Lysozyme}
However, for the first 3 pages of Tutorial commands only in the "Getting Started ..." tutorial, "cheat" by clicking on the solid green right-pointing single arrow head.
This will set you up for the Tutorial and will get the Lysozyme structure ...
You are urged to use the Lysozyme structure in this tutorial
for two reasons:
1) part of the tutorial focuses on the residues in the Active
Site ... which would be different for other molecules
2) another part of the tutorial focuses on "docking"
a polysaccharide lysozyme "substrate" to the molecule
... this would of course be incorrect for other proteins ...
The following is for any of you who do not want to "cheat" by using the green arrow head anyway:
1. In the command on page 2 of the tutorial (called "Protein
visualization ... Set up for the tutorial"), you have entered
the tutorial via the Pilot script and so you do NOT need to do
the "biosym_tutorial -i" command.
BUT you DO need to enter "insight" on the Command
line and do <Enter>...
2. Similarly in the command on page 3, after doing the menu
operations (Molecule/Get and choosing PDB as the
Get File Type, you need to type in the filename in the
Command line.
The filename is the name in the Tutorial Command: space, namely:
$BIOSYM/tutorial/insight/pdb6lyt.ent
If you have done this correctly, a stick model of lysozyme
will appear in the black graphic area of the Insight II window
...
{d. Include comments in your Notebook}
Include comments in your Notebook on steps that did not work, or that seemed unduly difficut to figure out ...
{e. Answer the Questions as you proceed through the Tutorial}
Latest modification: Spring, 2001
If you have problems or questions, send email to Michael
Gribskov or Doug Smith
or Hiren Patel