Spartan has two different interactive environments: the "Main" window, which allows us to manipulate the display of molecules and to set up calculations about the energies of molecules, and the "Builder" window, which contains the tools for constructing a wide range of organic and biological molecules. When you open Spartan icon, the program initializes and places you in the "Main" window. The menu bar at the top of the screen will look like:

Using the mouse, select New under the file menu. This will automatically bring up the builder window, which looks like:

The "model kit" on the right side of the screen contains tools we can use for constructing molecules in the workspace, and the "tool palette" on the left contains tools for manipulating these molecules. In the builder you have your choice of five different model kits to use: Entry, Expert, Library, Peptide, and Nucleotide. We will start with Entry, this model kit has the atom and the bonds configuration for making organic molecules.

Make enthane

Click on the carbon with four valences.

Click anywhere in the workspace, for the atom to show up in the middle.

Spartan automatically assumes that a free valence is a hydrogen unless you change it.

With the carbon still selected, Click on the end of one of the "free" valences to add another carbon atom.

It should look something like this:

Click anywhere on the workspace, and the bond will become solid.

To rotate molecule.

Using the middle button on the mouse, click anywhere on your workspace and hold.

Move the mouse to rotate your molecule.

To move molecule in window

Using the right mouse button, click anywhere on the screen and hold.

Move your mouse to move the molecule.

Energy Minimization

Every time after you "draw" a molecule you must minimize the energy for Spartan to show you find the conformation with the least strain energy.

Click on the minimize button near the bottom of the model kit.

The minimize windows should pop-up.

Click on the Continue button until Spartan won't let you click on it again.

For larger molecules it this would take a long time, so you can decide when to stop based on the energy values.

Click on OK

Measuring Distance

Select Distance, under the Geometry menu.

Instructions will be written on in the yellow space underneath the menu bar of the builder window.

Click on the two atom for which you want to know the distance between.

The distance will appear in the distance window.

Click on done.

Measuring Angle

Under the Geometry menu, select Angle, .

Instructions will be written on in the yellow space underneath the menu bar of the builder window.

Click on the three atoms for which you want to know the angle between.

The angle will appear in the angle window.

Click on Done.

Measuring Dihedral Angle

Under the Geometry menu, select Dihedral Angle, .

Instructions will be written on in the yellow space underneath the menu bar of the builder window.

Click on the four atoms for which you want to know the dihedral angle.

The angle will appear in the angle window.

Click on Done.

Constraining an Angle

Select Constrain Angle, under the Geometry menu.

Click on the three atoms of the angle you wish to constrain.

In the Constrain Angle Window, Click on the check box next to "Constrain Angle".

Click in the pink Constrain Angle box, and delete the current angel and type the new angle.

Click on OK.

To see the results of your constrained angle you must re-minimize your molecule.

Save it

Select save as, under the file menu.

Type in a file name, make sure your pointer in the box or else the SGI won't let you type.

Quit the builder, by selecting quit under the file menu.

Now you are in the main window.

Types of Models

Under the model menu, select Spacefill.

Select box, under model menu.

This may help you in keeping you orientation while rotating the molecule.

Play around with the different options under the model menu.

Continue with Tutorial

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Last revised February 23, 1998