BCMB8200, First Laboratory Exercises

Using Insight II, Modeling, Measuring and Surfaces

For preliminary instructions on Insight II see the Introduction page.

This first set of laboratory exercises is intended to introduce you to the molecular modeling suite, InsightII, and give you an initial experience in using it to manipulate and measure a protein structure. The second goal of the exercise is to have you create a Web-Report, a laboratory report published as a Web page.

PLEASE FOLLOW THE INSTRUCTIONS HERE CAREFULLY.

Creating a working directory:

To keep your disk clutter in control, it is best to use a separate directory for each laboratory of this class. For example, you might want to create a directory called "lab1" and then move to that directory before starting the program. The explicit instructions are as follows (where ..% is your Unix prompt):
..% mkdir lab1
..% cd lab1
..% insightII

After InsightII is loaded (be patient!), you will see a working window like the following:

As a convenience you may want to size the Insight II window and the netscape window side-by-side so that you can view both simultaneously.

GETTING AQUAINTED

From the "Molecule" menu (4th across top), select "GET"

Click on the button for PDB file type.

In the text box labeled "File Name", enter "/11/users/BCMB8200/lab1".

The second input window labeled "Parameters" will now contain a list of pdb files with short hand file names (e.g. 1cbp.pdb, 1crn.pdb, etc.).

Select the file insa.pdb from the list (last file).

Click the "Execute" button

Click the "Cancel" button

You should now have the wireframe structure of the insulin A chain displayed in your main InsightII window.

Moving, scaling and rotating:

CAUTION: With Insight you can change the structure using the left mouse button with selections involving some combinations of the others and keyboard keys (see Mouse Functions in the InsightII manual).
By default, the left mouse button selects atoms.
The right mouse button rotates the structure.
The middle mouse button moves the structure.
CENTER+RIGHT for Zoom (or Scale changes)
LEFT+RIGHT for rotations about the Z axis.
LEFT+CENTER for motion in Z.

Selecting atoms, residues and molecules:

The "selection level" and "selection style" menues (left screen margin) control how the left mouse button selects atoms, residues or entire molecules. In all cases, a click in the black void between atoms DESELECTS.
Use the "selection level" menu to investigate the different selection approaches.
With the selection level set to "ATOM," find a location on the molecule, place the cursor in the nearby black space and, holding the left mouse button down, drag a box around 2, 3 or 4 connected atoms. Now click the "Measure" button on the left margin and the appropriate measurement will appear (distance for two atoms, bond-angle for three and torsion angle for four). A SECOND CLICK on "Measure" will remove the measurement from the display.

Controlling the Display:

Coloring by atom type

Select the atoms to color (for example, with the selection_level set to molecule, a click on any atom selects all of them).
From the "Molecule" menu, select "Color"
From the "Color Molecule" menu, select the specification button,
then select "By Atom"
Select "Execute"
Select "Cancel"

NOTE the single disulfide bond (yellow color).
Changing how the atoms are displayed

Select the atoms to be changed
From the "Selection Render" menu , select the rendering method (CPK, Ball & Stick. Stick or lines).
Calculate and Display the Hydrogen Bonds

Select the "Measure" menu (top margin)
Select "H-bond"
Select the "Add" button (default)
Select "Execute"

NOTE the number of bifricated hydrogen bonds found by the selection criteria used by the program.
Clear display of H-bonds

Select the "Measure" menu (top margin)
Select "H-bond"
Select the "Clear" button
Select "Execute"
Examine the folding using a ribbon figure

Select the "Molecule" menu
Select "Ribbon"
Select the Solid_Rectangle under "Ribbon Style"
Select "Execute"

NOTE: the ribbon style can be modified with the other parameters in this window. For example, the ratio of the width to depth is altered by the XS Ratio parameter.
Clear display of the Ribbon

Select the "Molecule" menu
Select "Ribbon"
Select "Delete"
Select "Execute"
Displaying a Connolly Molecular Surface

Select the atoms for which you want to have the surface
Select the "Molecule" menu (top margin)
Select "Surface"
Select the "Create" button (default)
Select the "Connolly" button
Select the display Style (dots, big dots, line grid, solid)
Leave the surface quality low
Select "Execute"

NOTES on Surface Selections:

Atom Radius Scale is a multiplier for the vdW radii.
Atom Radius Incr is a fixed distance that is added to each atom's vdW radius.
Probe Radius is the probe used in the Connolly molecular surface algorithm.
The program documentation erroneously refers to the Connolly Molecular Surface as the Solvent Accessible surface.
However, solvent accessible surfaces (re. the Richards definitions) can be calculated by setting the Atom Radius Incr parameter to 1.4 and the Probe Radius parameter to 0.0.

Analyzing a structure:

You may measure a bond length, bond angle or torsion using either multi-atom mouse selection box (pull a box around the atoms) or using the "Measure" menu. For example, to measure a torsion angle:

select the "Measure" menu
select "Dihedral"
While you may enter the text descripton of each atom in the boxes labeled atom1, atom2, atom3 and atom4, it is simpler to click on the four atoms in succession.
Select "Execute"

NOTE: The results of the next two calculations are displayed in the Xwsh text window. It should automatically pop-up when you make the selections. However, if it has been minimized, you may have to click it open.
Listing the dihedral (torsion) angles of a protein.

From the MSI menu button (upper left-hand corner) select the Biopolymer module
Select the "Protein" menu
Select "List"
Select the "Dihedrals" button
Select "Execute"
If your Xwsh window is minimized, open it.
The table of dihedral angles is listed in the text window.
List the heavy-atom Hydrogen Bond distances

Select the "Measure" menu
Display and calculate the Hydrogen bonds using the "Add" and "Execute" buttons.
Select "List_Defined" from the "Monitor Mode" list at the top of the window.
Select "Execute"
View the H-bonds in the list in the Xwsh window.

Now take some time to investigate what you have learned about using InsightII.

You may want to try loading some of the other structures on the class directory or other functions than those discussed here. The program has a help function that is context sensitive. Click on the HELP menu item (Far right of top list, except in a case where you have resized and it may not be visible). Click on "Insight Help" and then as you click on menu items, you will see a small description of what each one does. At the submenu level, if the button at the top of the help screen is "depressed," a click on it will reveal an additional list of help topics for that item.

After you have investigated other Insight II features, click here to go to the Web-report exercise.

Return to the course home page.