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MolArch+ - Quick Start

This page gives a short introduction on how to use MolArch+.

You may also use the frames version of this documentation.

Top of Page MolArch+ - Quick Start
Quick Start

MolArch+ Window

To test the installation use the quick start below.
  • From a shell command line type (or copy-and-paste) the following command:
            molarch+ --pdbload $MOLARCH/examples/example1.pdb.gz --sldload
  • If everything is properly installed, you should get a MolArch+ window looking as displayed on the left. By the way, the structure on display is "Sucrose" with its dotted Connolly type molecular surface.
  • In case of problems check the MolArch+ - Error Messages.
General Usage
The following remarks may provide a short overview on the most important program characteristics of MolArch+.
  • When started from the console, all MolArch+ programs and sub-systems will print all information to the console (stdout), a wide text area with at least 140 columns is recommended for best reading of the output. All actions, calculated results, warnings, and errors are logged to the console. As a new MolArch+ user you may have to carefully read what is indicated here, in particular if you are not familiar with the general program behavior.

  • The graphics version of MolArch+ (molarch+) will give you a command line upon pressing any key that is not a macro-key as defined in the parameter file "molarch+.key", it is safest to use the space-bar. Commands may be entered on this command line and executed after hitting 'return'; the non-graphics version (molarch-) will read commands directly from the console (after the 'molarch->' prompt) or from stdin if invoked from within pipelines.

  • Shell special characters in commands and filenames (such as '*', '?', and '$') are expanded. If the first letter of a command is '>' or '!', the command is submitted to a UNIX shell (sh) and executed.

  • All commands, options and parameters (except filenames, numbers, and values) may be abbreviated using the first three letters only; anything else will be totally ignored. The above command 'pdbload' may be substituted simply with 'pdb'; type-setting errors such as 'pdbload' will also work as only the first three letters are interpreted.

  • All MolArch+ programs are case-sensitive when interpreting commands, options, and parameters. Generally these are all lowercase letters only, with some significant exceptions were the lowercase and uppercase keywords will behave differently (for example the command 'save pdb <file>.pdb' will not save bond records, but 'save PDB <file>.pdb' does; and calling the external POVRAY ray-tracing program by 'povray' or 'POVRAY' may produce different results). In any case, only the first three letters are interpreted. UNIX file names are generally case-sensitive.

  • The mouse-buttons are used as follows:

    • Left: Pick atoms and/or molecules.
    • Middle: Rotation around z-axis only.
    • Right: Rotations around x- and y-axis.
    • Left + Right: Move along x- and y-axis.

  • For a more detailed overview on program handling, commands, and options take a look at the file "molarch+.hlp" in your $MOLARCH installation directory.

  • Ctrl-c terminates program (key defined in the parameter file file "molarch+.key").

Program Options
MolArch+ options are stated on the console when starting the programs. These options start with a single dash '-'.
  • For a list of options see:
            molarch+ -h
Program Commands
MolArch+ commands (the 'long' commands differ from the 'short' options listed above) may be specified at program startup on the console or on the program-supplied command lines. If commands stated on the shell command line, each command must start with a double dash '--'.
  • For example the command
            molarch+ --pdbload example1.pdb.gz --sldload
    is identical to entering the commands
            pdbload example1.pdb.gz
    on the program supplied command line. This may be highly useful for automated tasks and shell scripts. Very long sequences of commands may be set-up and tested this way without re-typing commands, but by simply restarting the program with a modified command line. The MolArch+ - Examples on this web-site use such command lines and/or script files.

  • Please check the list of MolArch+ - Commands for an overview on the syntax and commands used.

© Copyright PD Dr. S. Immel