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Virtual Molecular Model Kit: Exercises |
Exercise 2 Return to Index
Introduction
The purpose of Exercise 1 was to provide you with the "roadmap" that Jmol employs and to illustrate how a model responds to different mouse movements. This exercise extends the ideas presented in Exercise 1 to situations where there are two "vehicles" on the road at the same time, i.e. two models in the Jmol window. We will encounter many such situations in future exercises. Developing control over the movement of models now will make completion of those exercises easier. Small images of the models made in each step or series of steps are provided in Figure 2.1 for comparison purposes. Clicking on an image will load an enlarged view.
Figure 2.1
Images of models involved in Exercise 2
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Steps 1-3 |
Steps 4-5 |
Step 6 |
Step 7 |
Step 8 |
Step 9 |
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Instructions
1. Start with: ethane.
2. Load a second model of ethane using either the Append:ethane command or the Compare:duplicate
3. Enter axes on in the Feedback & Script Command Field: and click Run Script
Note that Jmol places both models in the XY plane, the original model in the +X,+Y quadrant and the duplicate in the -X,-Y quadrant.
4. Activate the Model:move tool. Run the axes on script to display the axes again.
5. Superimpose the duplicate on the original; click on any atom in the duplicate model and drag the model onto the original.
6. Click/drag horizontally in the Jmol window to rotate the models around the Y axis by 90o.
From this perspective the X axis is projecting out of the plane of the Jmol window.
7. Click on the model and drag it horizontally to the left.
8. Drag the duplicate into the +X,-Y,+Z octant, i.e. drag it vertically down from its position in Step 7.
9. Click/drag horizontally in the Jmol window to rotate the models around the Y axis by 90o.
Comparing the first and last images in Figure 2.1 suggests that the duplicate model has simply been dragged horizontally from the -X, -Y quadrant into the +X, -Y quadrant. In fact, the copy is in the +X, -Y, +Z octant. Whenever you are driving, it's good to know where you are.
Like an automobile, the VMK has a dashboard. In fact it has four. They are called control panels; Draw, Edit, Tools, and Image. You will get a chance to try them out as you drive through the next 7 exercises.