Quick Guide to MacSpartan

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The very first rule to MacSpartan is: Don't have anything else running! These are PowerMacs, and they are wonderful tools, but MacSpartan will NOT run any calculations in a reasonable amount of time with anything else going on. Most of the time, MacSpartan won't even start a calculation with other applications running (the primary culprit here is Netscape... Don't even think about surfing while a calculation is running!). Also, be careful, if you make a molecule too large on screen (especially a space-filling model), MacSpartan can crash. So,

SAVE OFTEN!

Mouse and Keyboard Controls

Here is a short list of the most often needed keyboard/mouse commands:
OperationHold this key and mouse
Move on screenOption
Rotate in plane of screenApple
Rotate bondSpacebar
Zoom in/outOption and Apple

Remember that your mouse can be used to select areas of the screen and rotate molecules in some directions. Back to top

Molecule Builder

The molecule builder is opened when you request a new file or when you edit the structure of an existing molecule. In the builder, you have a workspace (black) on the left, a floating toolbar, and a molecule kit on the right. This kit contains all the "pieces" that will be used for your molecules. There are two sections to the kit; "Entry", and "Peptide". We will only use the Entry part. The Peptide kit contains amino acids, used to build proteins (large biologicals). Since we are concentrating on ab initio methods, we will not deal with proteins. In the Entry kit, there are fragments representing common atoms, as well as "Groups" and "Rings", which are preassembled functional groups. We will deal with building molecule from fragments for the majority of our time.

Below are a list of common actions in the Builder

Use the commands shown above to manipulate the fragments. Also, if you need more options, there are other commands under the Edit and Geometry menus of the Builder.

There are several fragments for some atoms, like carbon. This is because carbon can form different types of bond. Double or triple bonds are indicated by two or three lines on top of each other. MacSpartan automatically matches up multiple bonds.

When you are done making a molecule, click on Minimize. This will "bend" the molecule into a reasonable guess at the geometry.

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Menus

Model

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Geometry

The Geometry menu is designed to give you information about the molecule's current geometry.

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Build

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Setup

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Display

Be careful- if you define a new calculation and MacSpartan gives you a dialog box which says it will require "regenerating the wavefunction" etc., that means that you will not be able to display the results of the last calculation.

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Calculations

Hints and Troubleshooting

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