## 2. Windows and Help

If a window named inputlog.txt is open, close it. Before getting started, you will make a couple of settings that streamline intial program operation.

Prefs: General
On the General Preferences form, make the following settings:

- Uncheck "Show the 'setting depth to 256 colors'.. ."
- Uncheck "Show splash screen at startup."
- Uncheck "Show log file upon loading."
- Click OK.

On startup, DeepView opens two windows, the display or graphics window, which is labeled with the name of the PDB file (and the window size in pixels), and the Control Panel (on the right—if the Control Panel does not appear, use the command Wind: Control Panel to display it). The Control Panel lists the amino-acids residues and other contents of the PDB file. You use the Control Panel to select residues, establish the content of the display, label residues, and color them. Above the graphics window is the Tool Bar. You use the graphics window and the buttons on the Tool Bar 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. Other windows are available. You will now display them. The Wind menu allows you to open any of the DeepView windows, including the windows already mentioned.

Linux: Three windows open under Linux, the main Swiss-PDB application window (at the top), the Control Panel (on the right), and the black display/graphics window labeled "Swiss PDB Viewer accelerated with OpenGL". (The window behaviour may change depending on the setup of your X window manager. Most window managers offer three different "window activation" or "focus" policies: "ClickToFocus", "FocusFollowsMouse" and "SloppyFocus". The behavious described above is available when the "ClickToFocus" policy is in use.)

Wind: 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 DeepView, 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 DeepView commands affect only the selected residues.

Wind: 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.

Wind: 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. On Mac OS X, these help windows are also accessible from the Help menu. For more information about commands and functions, see the DeepView User Guide (pdf file), which you might HAVE downloaded with DeepView (if not, click here).

On the Tool Bar, below the first square button on the left (Zoom and Center), are two symbols, a globe and a little dog-eared piece of paper (document icon). Click the document icon 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.

### Review

- The Wind menu controls display of all DeepView windows.
- Each window has a small ? button that brings up help with using that window.
- You can change many aspects of DeepView behavior using dialogs available in the Prefs menu.
- For more information on any menu command, get the DeepView User Manual (pdf file), and see "Using the menus" in the section "Basic DeepView Commands."

For quick information about windows in DeepView, click on DeepView User Guide in the Contents frame (at left) and read General Information. Then click files and read the section entitled File Operations. This online user guide is not as up-to-date as the pdf user guide mentioned earlier.

Next Section: 3. Manipulating the Model

To The Molecular Level