Insight II, Run the tutorial on homology modeling.

This is to be done in Dr. Demeler's office on the SGI computer set up to run Insight II.  This computer runs UNIX, but you should be able to complete the assignment without having to learn about UNIX.  The assignment is to follow the InsightII homology modeling tutorial and make some screen shots for a presentation.  You should both explain  the  homology modeling process itself and describe the ease/difficulty of using the Insight II system.
 

Accessing InsightII

• To carry out this exercise, you will go to the Silicon graphics computer (SGI) in the back room of Rm 420D.  If you have difficulty, you can seek help from Dr. Demeler or Jeremy Mann in that facility, or from Dr. Hardies.
• Move the mouse to wake up the login screen, and then click on "Guest" to log in.
• This will allow you to run insightII as a user named guest.  This will be adequate for the purposes of this exercise.  You can recover any screen shot files you create by e-mailing them to yourself using webmail and the Netscape interent browser.
• For more serious use, you would need to have your own account and directory space on both the SGI and on bioinf.  These are free of charge to UTHSCSA personnel. Accounts can be requested here.
• Other access points are also possible, although requiring some effort to set up.  More information may be obtained from our collection of InsightII help files.
• After logging in, you will observe a desktop with the following:
• An icon named gimp: this program may be used to take screen shots. Detailed instructions are given below.
• A set of functions named "Toolchest" in the upper left corner".  The "internet" selection will run Netscape, which you can use to access these instructions, or other web pages, or webmail.
• A Console (or winterm) window.  If one is not present, open a new one by clicking on "desktop" in the Toolchest and selecting "Open Unix Shell".  You will use the Console/winterm window to start InsightII, but will not otherwise have to deal with it.
• Before proceeding, it may help to know that on the SGI desktop, the active window does not automatically come to the top of the display the way it does on most other systems.  Instead, you must right click on one edge of the window and select "Raise"  or "Lower" from the menu that pops up. Move the Console/winterm window so that it obscures the Toolchest and then try this out.

Familiarize yourself with the Insight tutorial system.

• In the Console/winterm window, start insightII by typing insightII.
• You can find the tutorials under "help" in the main window toolbar. Bring up the list of tutorials, and scroll down to "Homology tutorials".  Make sure "Run As Demo" is not checked (not yellow), and click <Select>.  Then select lession 1.
• Each time you click the green arrow in the upper left of the pilot window that appears, the tutorial will execute the last operation, display the results in the main window, and explain the next step.  Click through lessions 1 and 2 to get a feeling for the tutorial system.  These are about mechanical elements of the interface, and do not need to be part of your presentation.

Work through homology modeling in lession 3, and make screen shots to explain the process in your presentation.

• Here are some instructions on how to capture a screen shot.
• Click on the desktop GIMP icon.  You may have to "lower" or minimize the InsightII window to find it. Close all windows that GIMP opens except the small window with a pallet of tools and a toolbar reading: <file><Xtns><Help>.  Position it at the left of the desktop so that the <file> toolbar item is visible when the IinsightII window is brought back to the top of the display.
• Arrange the other windows the way you want them for a screen shot.  In the example shot linked below, I had just proceeded to the first images loaded by the lession 3 tutorial.
• Click <file> on the Gimp toolbar, then <acquire> <screenshot>
• Give yourself about a 4 second delay, decide if you want a window or the whole screen, then click OK.  If you chose a single window, you'll have 4 seconds to click in the desired window.
• When a new GIMP window appears containing the captured image, right click on it.  This will give you a popup menu from which to save the image.  Saving with the extension .bmp will give about a 4 Mb high resolution image.  Saving with extension .png gives a good image of about 200 K.  When the png parameters window pops up, turn off all the parameters and set compression level to 1.
• The .bmp files are Miscrosoft's native format and should work fine with Microsoft presentation software.  The large size may give you trouble if you try to send them through university webmail.  If you use Biochemistry's webmail instead, there should be no problem as long as you send them one at a time.  .png files get along with most software, and are small enough to fit in the tiny space allocated for attachements by university webmail.
• Here is an example screenshot after loading the first images in lession 3.
• Here is how to resize or rotate the molecule to prepare for the screen shot.
• The image loaded at first in lession 3 needs to be scaled down to fit it in the window and see what it looks like.
• Find the panel at the lower left of the main insight window that has "X rotate", "X translate", etc.
• These are sliders.  For example, clicking on the left side of "world scale" causes the image to get smaller; clicking on the right side of "world scale" causes it to get larger.  Familiarize yourself with these controls.
• Here is another screen shot after resizing the initial image that was loaded in lession 3.  Since I am making an html presentation, I used Microsoft Paint (found in <start><Programs><accessories>) to convert my images to .gif files.  .gif format is universally recognized by all web browsers, and is of a compact size that loads quickly.  One was e-mailed out as a .bmp file, and the other as a .png file.  Unfortunately, GIMP will not directly save a color .gif file.  If you use other presentation software, like Microsoft Powerpoint, you may have to experiment on how to get images converted without loss of quality.