Insight II Notes: Viewer

The Insight II Window

All menus are fairly straightforward, and the manuals provide a good description of these menus. BE CAREFUL to review ALL selections in the menu before executing your selections. Remember that this program is designed to analyze a wide variety of molecules, so defining specific commands for specific parts of molecules can be a detailed process.

The following is an example of how the menus can be used to execute commands:

Click the left mouse button on the Molecule pull-down. Click on Get Molecule. Click the button next to PDB. Click on User Directory. All files that end with the .pdb extension in the directory from which you started InsightII are shown. Click on the file that you want to read into the program. Notice the other choices that you can make in the Get Molecule menu. Click on execute, and the molecule is read into the program.

The screen has a variety of tools around the edges:

• The current module name is always listed at the top.
• The Logo button (blue and white square in upper left corner) also serves as the Module Icon. Click on the Module Icon to view a list of modules (some modules which are listed MAY NOT WORK. Consult the License Table for a list of licensed modules).
• Several of the most common commands can be accessed through the icon palette at the left edge of the window.
• The Dial Slider Box can be used to move objects, and is described under Moving Objects. The box below the Dial Slider Box lists the connected object.
• The Command Prompt awaits your typed commands at the bottom of the screen, but is not often used.
• The Information Area displays messages from the program. For instance, position your mouse cross-hairs over an atom and click the left mouse button, the atom specification (see below) appears in the Information Area.
• The on-screen function keys and the keyboard function keys have the same performance. For example, click on the Textport On button (or type the <F9> key). The textport window comes to the front of the screen, which is also an information area. Click on Texport Off (or type the <F9> key) to move the textport behind the InsightII window. More function keys are listed under Moving Objects.

Some menus have boxes which have pre-defined sets of atoms and choices. Click around in these menus and windows to select these choices. For instance, click on molecule/color. Type in the molecule name in the Molecule Spec box. Click on the box under color. The color palette will appear. Move the slide bars to create a new color, or click on a colored square to select a predefined color. The click on execute and the backbone of your molecule will change color.

The Molecule Pick Level can be used to select all or parts of a molecule:

• To select the entire molecule, click on the small box next to molecule in the Molecule Pick Level menu, then click on an atom in your molecule. The name of the molecule will appear in the Molecule Spec Box.
• To select a (pre-defined) subset of the molecule, click on the small box next to subset in the Molecule Pick Level menu, then click on an atom in the subset. The name of the subset will appear in the Molecule Spec Box.
• To select a monomer or residue of the molecule, click on the small box next to monomer/residue in the Molecule Pick Level menu, then click on an atom in the residue. The name of the residue will appear in the Molecule Spec Box.
• To select a single atom of the molecule, click on the small box next to atom in the Molecule Pick Level menu, then click on the atom. The name of the atom will appear in the Molecule Spec Box.

The monomer/residue specification can be:

• a specific residue type such as LYS
• a specific residue, such as A312 (residue 312 of the A-chain)
• a range of monomers such as A312-A350.
• several monomers such as A312, A215, A345, A350
• the special names BEG or END, the first and last residue
• every nth residue, such as A312-A340@2 specifies every other residue started with A312 and ending with A340
• a combination of the above, such as LYS, A312-A315, A345, END
• all atoms can be specified by '*', or by not specifying anything.

If these three parts of the Focus are put together, parts of the molecule can be specifed.

Examples:

Crambin:1:ca

specifies the alpha carbon of residue 1 in Crambin

Crambin:1-10:c*

specifies all carbons in residues 1 to 10 in Crambin

*:2,10,33,35: c1,c3

specifies carbons 1 and 3 of specific residues in ALL molecules

Crambin:ARG:hn,n,ca,c,o

specifies all backbone atoms of all arginine residues in Crambin

Crambin:BEG-10;*

specifies all atoms from the first to the 10^th residues in Crambin

Crambin:BEG-END:*

specifies all atoms in Crambin

Crambin:*:*

specifies all atoms in Crambin

Crambin::

specifies all atoms in Crambin

Crambin

specifies all atoms in Crambin

*

specifiels all atoms in all molecules

WARNING! Some molecules, such as the DNA double helix, are composed of TWO molecules that are NOT connected be a covalent bond. To move the two molecules together:

• Click on Transform/Connect, click on Assembly in the Molecule Pick Level menu, and select the assembly containing the two molecules. If you don't know the name of the assembly containing the molecules, click on Assembly/List.
• In the Builder or Biopolymer menu (to load these menus, select them from the Logo/Module Icon) , click on Modify/Merge, and merge the two molecules together (the name of the resulting single molecule will be the name of the first molecule specified). The program will then think that the two molecules are just one molecule.

To move a connected object or world, hold down a combination of mouse buttons and move the mouse. The x-axis is horizontal and the y-axis is vertical in the plane of the screen. The z-axis comes straight out of the screen.

In the lower left corner is a "dial slider" box. Position your mouse near the MIDDLE of the X rotate box and click and hold down the left button, and the molecule will rotate. Move the mouse SLOWLY to the left or right inside the X rotate box. As you move to the edges of the X rotate box, the rotation speed increases. The center of the box is "rotation speed=0". The slide boxes are sensitive and tricky, so be careful.

The function keys can also be used. You can also click on the buttons at the bottom of the screen, which act like on-screen function keys. Some function keys are not active unless you are running a specific application:

Finally, molecules can be moved by using the Transform menus. These menus can accept values for exact placement or movement of a molecule. Other objects can be moved using other pulldown menus.

Use file/Save Folder, which saves the position, color, labels, etc., of all objects that you specify. You should save all objects ('*'). Choose a new file name each time you save a folder; you can delete old, unnecessary folders in a UNIX shell after you are done. DO NOT use the replace option! This option replaces objects in a current folder if the object exists in the folder; if the object doesn't already exist in the folder, the object is NOT saved.

You can also use the Session/Autosave (which is turned off by default) or Session/Backup and Session/Recover options. Session/Autosave allows your session to be automatically saved at regular time intervals. The session is saved to a file called ".insight_session.psv".
SAFETY TIP: In a UNIX shell, you must type "ls -a" to list files that start with a period (".")

Commands are stored in a file named WBLOGFILE. When you gracefully exit the program using quit, WBLOGFILE is renamed insight.log. If the program crashes or you exit ungracefully by closing the window, WBLOGFILE is NOT renamed. If you restart InsightII and you have a file named WBLOGFILE, the program will rename WBLOGFILE to WBLOGFILE.save and will start to log new commands into a new WBLOGFILE. Thus, you can compare WBLOGFILE and WBLOGFILE.save to determine if your problems are indeed reproducible. If the program crashes, type cp WBLOGFILE new_file_name so that you have a more permanent record of your problem, so that you can more easily troubleshoot your problems.

You can also make your own log file (the file name must end with .log) in UNIX using your favorite editor (ie.g., nedit, jot, vi). See also the Example InsightII log file. In InsightII, click on File/Source File, select your log file, and InsightII will run these commands. This is a nice way to set up a demonstration of your work!

To execute commands each and every time you start InsightII, create a file in your home directory named .insightII.cshrc See the .insightII.cshrc example file. This is a great way to customize your InsightII environment; for example, you may wish to automatically set Molecule/Bond_order ON (the default is OFF) to display bond orders, create aliases for common commands, or set the default z-plane clipping.

You can modify InsightII's menus and icons in several ways:

• Use Session/Cmd_display to change how each command's parameters are displayed
• Use the commands in the Window menu to control the location, size, and other features of windows in InsightII.
• Use Session/Button to create your own icon buttons on the left side of the screen.

The Session/Help feature is accurate, but often devoid of detail. Consult the manuals in A701 for more information. Although computer manuals are notoriously convoluted, Biosym manuals are extremely well-written.

When you use a pulldown menu, you select options that build a string of commands. When you click on execute, this command is sent to a module, and the module performs the operation. These commands are displayed in the Information Area. They can be accessed by typing the following 'history' keys:

History Features