Rama Plot:

When this is selected, the user is asked for a residue range of the protein. A window then opens and a Ramachandran plot is displayed with the various Phi-Psi values plotted. The GLY residues are orange dots and the PRO residues are purple boxes. If a Ramachandran window is already open when this option is selected, then the plot is simply redrawn. To do a different zone, you need to close the Rama window first and select this option (close window by hitting the small box in the upper left corner of the widow). This window can be re-sized by dragging the box in the lower right hand corner. !!The font selected by the Labeling menu is used for this diagram as well.

Pick Rama Points:

This option displays the residue number of each point on the Ramachandran plot when selected by the mouse. Couple of things to note: If this option is toggled on, then you are not allowed to put the other window in front or to work on the atomic model window. You need to toggle this option off and then work on the other window (or select some of the other options on the other window like 'Hand Pick Atoms'). Also, the numerical values are not saved on the plot. You can clear the numbers by selecting the 'Rama Plot' option again.

Plot Preferences:

This option opens a window that displays the current settings of the Ramachandran plot routine and allows the user to change them. It allows the user to display the boundaries of the allowable zones and allows the user to switch between color and B&W diagrams. For B&W diagrams, GLY residues become filled black circles and PRO residues become square, gray blocks.

See Movie:

This is a fairly useless option, but was only a couple of lines of code--so what the heck. When you select this option, you are given the same dialog box found in the 'Rotate' option. You can input the rotation you wish each step of the movie to be. After this, the objects that are currently selected begin to rotate. To stop the movie, just click the mouse within the window.

Make Movie PICTS:

This is the same as the last option except that for each rotation, a PICT file is written out. The process continues until the mouse is clicked on the image. The files are created in the local directory and start with the name 'Frame0' and numbered sequentially after that. We have used this option to readily create a movie using MacroMind Director. Remember to use the 'User Set Back and Clip' option (under the 'Misc.' menu) to draw the size and shape background you would like for the movies. This latter option is really essential for making movies.