Select, display, and center the complete model. Color backbone and sidechains CPK.
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 click any atom (if in stereo, click the left image). Next, following the instructions that appear in the message space at the bottom of the Tool Bar, click another, distant, atom (left image in stereo). After you have clicked two atoms, you learn the distance between them. The distance is shown as a label, along with a dotted line. Again, following the instructions in the message space, pick another pair of atoms to display a second distance.
As you move the cursor to use measuring tools, the message area underneath the Tool Bar buttons shows you the identity the last touched atom, along with its coordinates and B-factor (a number related to the accuracy of the atom's position in the model). This aids you in finding the desired atom before clicking it.
Pressing the escape key turns off a measuring function. During measuring functions, movements are still available, as long as the click to start the movement is not on an atom.
Remove the distance label as follows:
Display: Labels: Clear User Labels (or command -)
Labels added as a result of measurement are called "user labels", to distinguish them from the group labels that are applied by the Control Panel labl column.
Use the distance button to determine the approximate length and thickness of lysozyme. (How might you use slabbing to help you make sure you measure through the center?)
Then remove the distance labels. Press esc to turn off measuring.
Next select, display, and center a few residues, and click the angle button. As DeepView 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. DeepView adds the angle as a user label. The three atoms need not be connected, so you can measure angles made by distant groups in a protein. Turn off the angle function (esc).
Now click the dihedral-angle button and then click on any residue. In the message space on the Tool Bar, DeepView displays the omega, phi, psi, and omega angles (omega or w is the dihedral angle of the peptide bond, usually close to 180 degrees). This display persists only as long as you hold the mouse still. When you then move it over other atoms, Deepview resumes the display of the atom last touched with the cursor. Turn off the function, hold down control and click the dihedral-angle button again. Following the instructions, pick four successive atoms on a side chain. DeepView reports the dihedral angle (as long as you hold still after the last click). With this feature, you can measure any dihedral angle, even arbitrary ones involving non-connected atoms. esc turns off this function also.
Linux: control functions may be missing.
Test your understanding of phi and psi angles by measuring them with and without the control key.
With any of these buttons, DeepView allows you to make repeated measurements without clicking the button for each one. When you have completed your measurement, or if you decide not to complete an individual measurement, esc resumes normal use.
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. You can continue labeling, as you might if you are looking for a particular residue. As with measuring functions, esc ends this function. The labels applied are also user labels. Remove them the same way you removed the distance labels above.
Take time to PLAY with the tools introduced in this section.
To The Molecular Level