# Starting

## UNIX

MOLMOL is supplied with a shell script (`molmol` in the top level installation directory) that processes options and arguments and sets the necessary environment variables. The following options are recognized by this shell script:

> argument | description
> --- | ---
> `-h` | give list of options
> `-t` | TTY interface (no graphics)
> `-o name` | alternate input/output device
> `-2` | stereo mode (OpenGL only)
> `-a` | display all atoms (not backbone only)
> `-s` | superimpose complete backbone
> `-r range` | superimpose given backbone range
> `-f file` | execute macro file (`-` for standard input)
> `files` | DG, PDB, Angle or Dump files

If the program is started without names of structure files, it will recover the saved state of the last invocation (if available) and ignore all options but `-f macro`.

Besides the listed options, the program will also recognize standard Xt options, like `-bg color` for setting the background color.

## Windows

Under Windows, you will normally start MOLMOL by double-clicking its icon (a capital M in cyan and red). You may want to create a shortcut on your desktop. Right-click on the icon e. g. in Windows Explorer, select "Create Shortcut" in the menu, and drag the shortcut to a convenient location on your desktop.

The following command line options are recognized:

> argument | description
> --- | ---
> `-stereo` | stereo mode
> `file` | execute macro file

If you want to use one of these options, you can either start the executable from a command prompt, or define a shortcut, and then set the argument in the properties of the shortcut (right click on icon, select "Properties", click on "Shortcut" tab, and add the argument after the executable in the "Target:" field).

You can also start MOLMOL by defining it as program to be started for files with a certain exptension (like `.pdb`), and then double-clicking a file with this extension.

MOLMOL also supports drag and drop for some common molecule file types. If a file with one of the following extensions is dropped into the main window of the running program, the file is loaded with the corresponding command:

> extension | description
> --- | ---
> `.pdb` | `ReadPdb`
> `.ent` | `ReadPdb`
> `.cor` | `ReadDg`
> `.mol2` | `ReadSybyl`
> `.ml2` | `ReadSybyl`
> `.xyz` | `ReadXyz`
> `.ang` | `ReadAng`
> `.seq` | `ReadSeq`
> other | `ReadDump`

Last modified: Mon Jan 20 19:44:55 CST 2003