# Main Window Elements

The following image shows a screen dump of the MOLMOL main window, with annotations for its elements. Each of them will be briefly explained in the following sections.
When you start up MOLMOL for the first time, you will see two dialogs boxes in addition to the main window. If you prefer not to see them each time you start the program, you can disable them using the `UserInterface` command, and choose the option to save the program state when you quit the program. You can do the same if you do not want certain parts of the main window to appear.

## Drawing Area

All graphical display of molecules (and other items) will appear here. You also use this area for interactive mouse manipulations, like zooming and rotating.

## Menu

The menu contains all MOLMOL commands, you use the common navigation methods known from other programs to access commands in the menu. The following is a short overview of which kinds of commands can be found in which pulldown menu:

File
  Input and output of files. This includes reading and writing of molecules in many formats, output of plots, execution of macros, and a variety of other commands.
Edit
  Commands that modify molecules. This includes commands that change the covalent structure (adding and removing atoms and bonds, building molecules from residues, etc.) and commands that modify coordinates (rotation, translation, changing dihedral angles, superposition, etc.).
View
  Commands that change global viewing parameters. This includes zooming, camera and light source parameters, clipping planes and fog.
Options
  Commands that change various kinds of configuration options and preferences. This includes the choice whether certain dialogs are displayed, selection of stereo and animation modes, rendering options, display quality, plot parameters, and path names of configuration files.
Prop
  Commands that change or list properties. Properties are boolean values that can be set for various data items, they are mainly used for Selection.
Attr
  Commands that change graphics attributes, like colors, display styles, material properties, etc.
Calc
  Commands that perform calculations. A large variety of calculation and analysis possibilites for molecules can be found here.
Prim
  Commands that create and modify primitives. Primitives are things that can be displayed, but are not molecules. This includes annotations, schematic displays (ribbons) and surfaces.
Fig
  Commands that draw figures used for the analysis of molecules. This includes Ramachandran plots, angle distribution plots, contact maps, etc.
Opt
  This menu appears when optional commands are defined as part of the startup macros, and those commands are not contained in any other menu. See the section on configuration for information on how to extend the program with optional commands.
Help
  Commands for access to various forms of online help.

## Buttons

The buttons give quick access to some frequently used (combinations of) commands. You can use the `HelpButton` command to see how exactly the buttons are defined.

## Command Line

As well as selecting them from the menu, all commands can also be entered on the command line. Parts of commands that are unique are completed automatically while typing. You can also enter command arguments on the command line.

## Status Line

A short help message is displayed here while the mouse pointer is moved over menu entries or buttons, or when a command is entered on the command line. Some commands also display informative messages on the status line.

## Break Button

Most long running commands can be interrupted by clicking the mouse on this button. The button will be active while such a command is running, inactive (grayed out) otherwise.

Last modified: Mon Jan 20 19:44:56 CST 2003