Exercise 1 Return to Index
This is the first of a series of 9 short exercises designed to introduce users to most of the features of the Virtual Molecular Model Kit; how to "drive" the VMK if you will. Driving the VMK is easy. While most of the commands are self-explanatory, the way in which the models respond to the "steering wheel", i.e. movements of the mouse, may be confusing at first. To understand those movements it is necessary to understand the coordinate system that Jmol uses when displaying models. The purpose of this exercise is to demonstrate the relationship between the movement of the coordinate system and that of models displayed in that coordinate system.
1. From the Molecular Editor control panel select Start with: ethane.
2. Enter the command axes on in the Feedback & Script Command Field: and click Run Script
Note how Jmol's coordinate system is oriented: the X and Y axes lie in the plane of the Jmol window with the Z axis perpendicular to that plane; the X axis is co-linear with the C-C bond axis, while the Y and Z axes are perpendicular to the mid-point of the C-C axis. When a model is loaded into the Jmol window, the program positions the "center" of the model on the origin of the coordinate system.
3. Click/drag horizontally in the Jmol window to rotate the model around the Y axis.
4. Click/drag vertically to rotate the model around the X axis.
5. Alt-click/drag horizontally to rotate the model around the Z axis.
Because Jmol positions the "center" of the model on the origin of the coordinate system, the model remains centered in the Jmol window during the rotations in steps 3-5. If you move the model away from the origin, its position no longer tracks that of the origin during these rotations:
6. Reload the model of ethane using the Start with: tool.
7. Activate the move option of the Model: tool.
8. Run the axes on script.
9. Click on any atom in the model and drag the mouse toward the +X,+Y quadrant.
10. Now observe how the model moves when you repeat steps 3-5.
Exercise 2 extends the ideas presented in this exercise to situations where there are two models in the Jmol window. But before beginning that exercise, consider one additional feature associated with click/drag movements of the mouse; zoom.
11. Reload the model of ethane.
12. Shift-click/drag vertically from the top of the Jmol window toward the bottom to zoom in on the model. Dragging from the bottom towards the top will zoom out.
Now that you've taken the VMK for a spin, you're ready to learn about its built-in "GPS", in other words, you're ready for Exercise 2.