Back to TABLE OF CONTENTS  General Operations:  Part 1   Part 2
General Operation
Topics in General Operation Part 1:
· Running RasMol Under UNIX or VMS
· Running RasMol Under Microsoft Windows
· Running RasMol on the Apple Macintosh/PPC
· RasMol's Window and a page on the Pull Down Menus
· Mouse Controls
Topics in General Operation Part 2:
· Scroll Bars
· Picking
· Dials Box
· Command Line Interface
· Dimensions within RasMol
· Start-up Initialization Files
· Inter-Process Communication (IPC)
Running RasMol Under UNIX or VMS
   To start RasMol from either the UNIX or VMS prompt, type the command 'rasmol'. This command can be followed by an optional filename. By default, immediately upon starting, the program displays the following message to identify the version number and display depth of the running program:
     RasMol Molecular Renderer
     Roger Sayle, October 1994
     Version 2.5
     [8bit version]
   Immediately underneath this banner message appears the program's command line prompt 'RasMol>'. If the program is being executed under the X Window System, the program determines the type of the display being used. If the screen has either an 8 bit or 24 bit color frame buffer, RasMol creates another window, which is used to display menu options and the rendered images. If a suitable screen is not available, RasMol may only be used from the command line. Commands may be typed to manipulate the model, and to output the generated image to a raster file.
   If the program is run under the X Window System environment with a suitable color screen, RasMol creates an additional window to display the rendered molecule interactively, as it is manipulated. If RasMol is not run under the X Window System, the program displays the message 'No suitable display detected!'. RasMol may be instructed not to display a graphics window by using the command line option '-nodisplay'. This is particularly useful for using RasMol as a background or batch process.
   It is possible to specify either a coordinate filename or a script filename or both on the UNIX/VMS command line. The format for specifying a script file is to add the option '-script<filename>' to the command line. A molecule co-ordinate file may be specified by placing its name on the command line, optionally preceded by a file format option. If no format option is given, the specified co-ordinate file is assumed to be in PDB format. Valid format options include '-pdb', '-mdl', '-mol2', '-xyz', '- alchemy' and '-charmm', which correspond to Brookhaven, MDLMol file, Sybyl Mol2, MSC's xyz, Alchemy and CHARMm formats respectively. If both a co-ordinate file and a script file are specified on the command line, the molecule is loaded first, then the script commands are applied to it. If either file is not found, the program displays the error message 'Error: File not found!' and the user is presented the RasMol prompt.
   In order to leave RasMol, the user can type the command quit or exit at the RasMol prompt, and the program will return the user to the familiar unix prompt. Alternatively, if a prompt other than the main RasMol prompt is being displayed, the user may hit control-C (^C) to leave the program. The message '***Quit***' will be output to the terminal, before the usual unix prompt is redisplayed. The program may also be terminated by selecting the Quit menu option, on the bottom of the main menu.

Running RasMol Under Microsoft Windows

   To start RasMol under Microsoft Windows, double click on the RasMol icon in the program manager. When RasMol first starts, the program displays a single main window (the display window) with a black background on the screen and provides the command line window minimized as a small icon at the bottom of the screen. The command line or terminal window may be opened by double clicking on this RasMol icon.
   It is possible to specify either a coordinate filename or both on the windows command line. The format for specifying a script file is to add the option '-script <filename>' to the command line. A molecule co-ordinate file may be specified by placing its name on the command line, optionally preceded by a file format option. If no format option is given, the specified co-ordinate file is assumed to be in PDB format. Valid format options include '- pdb', '-mdl', '-mol2', '-xyz', '-alchemy' and '-charmm', which correspond to Brookhaven, MDLMol file, Sybyl Mol2, MSC's xyz, Alchemy and CHARMm formats respectively. If both a co-ordinate file and a script file are specified on the command line, the molecule is loaded first, then the script commands are applied to it. If either file is not found, the program displays the error message 'Error: File not found!' and the user is presented the RasMol prompt.

Running RasMol on the Apple Macintosh/PPC
   To start RasMol on the Macintosh, double click on the RasMol icon using Finder. When RasMol first starts the program displays two windows, the top window (with the black background) is the graphics or canvas window and the window underneath it (with the white background) is the RasMol command line window.
   RasMol on the Macintosh may also be started by double clicking on a file owned/created by the application with the signature 'RSML'. This will start up RasMol and pass the selected file to be loaded. There is no way of specifying the file format on the command line with a Macintosh so RasMol attempts to determine the file format by inspecting the file's type signature. Files with type signature 'RSML' are assumed to be RasMol scripts, files of type 'mMOL' are assumed to be MDL Mol files and all other types (principally 'TEXT') are assumed to be in PDB format. Unlike other versions of RasMol it is impossible to specify both a script and a coordinate file simultaneously.
   Dragging and dropping multi-file 'movie' scripts onto aliases or copies of the RasMol application file may fail due to confusion about which is the correct script folder. Double-clicking on a script may lead to similar problems if copies are present. Further information will be found in the 'movie' script operation document , where you will find reference to an explanation of Macintosh signatures and how to change them.
   Note that because on a Macintosh only one 'instance' of an application may be running at any one time, if you were double click on another file owned by 'RSML', the running copy of RasMol would zap its molecule and load the newly specified file.

RasMol's Window
   On all platforms RasMol displays two windows, the main graphics or canvas window with a black background and a command line or terminal window. At the top of the graphics window (or at the top of the screen for the Macintosh) is the RasMol menu bar. The contents of the menu bar change from platform to platform to support the local user interface guidelines, however, all platforms support the 'File', 'Display', 'Colors', 'Export' and 'Options' pull-down menus. (See the page on RasMol's Pull-Down Menus for a description of the selections available on the Macintosh.) The Main graphics window also has two scroll bars, one on the right and one at the bottom, that may be used to rotate the molecule interactively.
    The Macintosh implementation lacks the built-in hypertext help available from the 'Help' menu under MS Windows. The 'help' command is available in the command line window provided that the file 'rasmol.hlp' is in the same folder as the application itself, but this may be relatively cumbersome to use. Therefore it is recommended that the present hypertext manual be brought up in a web browser window when help is needed on the Macintosh. Since in RasMol 2.6 beta-2 the built-in hypertext manual is still at version 2.5, this is recommended for other operating systems as well. A local copy of this manual can be saved from the File menu in the web browser, and can be viewed in the browser's local mode even on computers lacking an Internet connection.
   While the mouse pointer is located within the graphics area of the main display window, the mouse pointer is drawn as a cross-hair cursor, to enable the picking of objects being displayed; otherwise the mouse pointer is drawn as an arrowhead. Any characters that are typed at the keyboard while the display window is in 'focus' (meaning active or foreground) are redirected to the command line in the terminal window. Hence you do not need continually to switch focus between the command line and graphics windows.
   The display window may be resized at any point during the session. This has the effect of simply rescaling the image displayed on the canvas. RasMol imposes limits on the size of the display window such that the window must be large enough to display the menu and scroll bars and yet small enough to fit on a single screen. Attempts to enlarge the screen may fail owing to insufficient memory on the host machine, in which case RasMol reports the error message 'Renderer Error: Unable to allocate frame buffer!' or some similar error.
   On eight bit displays, when the number of colors required by the program exceeds the number of free colors on the screen, the program uses its own colormap. This has the effect of temporarily displaying all windows other than the display window in false colors while the mouse pointer is within the display windows. If the mouse pointer is moved outside the display windows, the original colors of the other windows return, and the image on the canvas is shown in 'false color'. Once the number of colors required by the program drops again, the presentation of colors returns to normal.

                                               Mouse Controls
   Here is a summary of RasMol's mouse click-and-drag controls. The set mouse command mode defaults to set mouse rasmol, which gives the controls summarized below. However, there are also set mouse insight and set mouse quanta modes (not shown below).
*On some Macs, the Option (Alt) key has the same effect on RasMol as the Command key.
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