SPdbV opens two windows, the Control Panel (on the right), and the display or graphics window, which is labeled with the name of the PDB file (and the window size in pixels). The Control Panel lists the amino-acids residues and other contents of the PDB file. You use the Control Panel to select residues, determine the content of the display, label residues, and color them. You use the graphics window and the buttons at its top to view, manipulate, and measure the model. You must click on a window to make it active. The first click on an inactive window activates it, but does not cause other changes. Three other windows are available. You will now display them. The Display menu allows you to open any of the SPdbV windows, including the windows already mentioned.
Display: Show Sequences
Alignment
The narrow Align window appears below the graphics
window, showing the amino-acid sequence of the protein in one-letter
abbreviations. You use this window when comparing sequences of two or
more proteins.
NOTE: Whenever you quit SPdbV, it remembers which windows were open and their locations. So if you have already run the program before you started this tutorial, window locations may be different from those stated here.
Select: All
The color of residues listed in the Control Panel changes from
black to red (and in the Sequences Alignment window, from white to
purple). The new color means that a residue is currently selected.
Some SPdbV commands affect only the selected residues.
Display: Show Ramachandran Plot
The Ramachandran Plot window appears in the upper
left. You can use this window to judge the quality of a model, by
finding residues whose conformational angles lie outside allowed
ranges. You can also display and change conformational angles in the
model. Each dot (actually, a tiny cross or square) on the diagram
gives the phi and psi angles of one residue in the protein. Because
all residues are selected, all are represented in the
window.
Display: Show Layer Infos
The small Layer Infos table appears at the upper
right. This table provides control of multiple protein models,
allowing you to choose which models are visible, which models can
move, and which models have certain features on display.
Each window displays a small red question mark. Click the question mark for help in using that particular window. For more information about commands and functions in the full User Guide for SPdbV, look under the Apple menu (Help menu on PC). Select WWW Manual, and your web browser will automatically connect to the User Guide at the SPdbV Home Page. If have downloaded separately and installed the folder _stuff_ in your SPdbV folder, and you prefer to read the manual without connecting to the web, choose Local Manual. Browse around to see how the guide is organized. The Index is very handy for finding out more about specific commands.
On the graphics window, below the first button on the left (Window Attributes), are two symbols, a globe and a little dog-eared piece of paper. Click the paper to see the PDB file of the protein currently on display. This file will come to mean more to you later, but if you are curious about it now, see PDB File Contents. Close the file window before proceeding.
For now, close the Align, Ramachandran Plot, and Layer Infos windows.
For more information about windows, click on SPdbV User Guide in the Contents frame (at left) and read General Information. Then click files and read the section entitled File Operations.