Select, display, and center the complete model.
To the right of the movement buttons on the graphics window, the next three buttons (five, six, and seven from the left) are for measuring distances, bond angles, and dihedral angles. Click the distance button, and then, following the instructions that appear in the message space above the model, click another, distant, atom (left image in stereo). After you have clicked two atoms, you learn the distance between them. Remove the distance label as follows:
Display: Labels: Clear User Labels (or command - [the minus sign on either the main keyboard or the keypad])
Use the distance button to determine the approximate length and thickness of lysozyme. (How might the use of slabbing help you to make sure you measure through the center?) Remove the distance labels. If you want to make several distance measurement, press caps lock. As long as the caps lock function is on, SPdbV continues asking you for distances to measure. Press escape or release caps lock to turn off measuring.
Next select, display, and center a few residues, and click the angle button. As SPdbV instructs in the message space, pick three atoms that define the angle you want to measure. First, pick the center atom, and then pick two atoms connected directly to it. SPdbV prints the bond angle at the top of the window. The three atoms need not be connected, so you can measure angles made by distant groups in a protein.
Now click the dihedral-angle button and then click on any residue. In the message space below SPdbV displays the phi, psi, and omega angles (omega or w is the dihedral angle of the peptide bond, usually close to 180 degrees). Now hold down control and click the dihedral-angle button. Following the instructions, pick four successive atoms on a side chain. SPdbV reports the dihedral angle. With this feature, you can measure any dihedral angle, even arbitrary ones involving non-connected atoms. Test your understanding of phi and psi angles by measuring them with and without the control key.
With any of these buttons, caps lock allows repeated measurements, and if you decide not to complete a measurement, escape resumes normal use. You cannot manipulate the model (or leave SPdbV for another program) until you complete or escape the measurement, so arrange the model so you can see all desired atoms before starting to measure.
Look at the remaining buttons at the top of the graphics window. Click on the button labeled LEU41? Then click on any group to learn its identity and label it. After SpdbV adds the label, it turns off the labels button. If you want to continue labeling, as you might if you are looking for a particular residue, press caps lock and then click the labels button. Now SPdbV labels every atom you click until you press escape. Remove the labels the same way you removed the distance labels above.
Take time to PLAY with the tools introduced in this section.