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MolArch+ - Parameter Files and Settings

This list gives a short description on the various user-accessible parameter files and settings used by MolArch+.

You may also use the frames version of this documentation.

Top of Page MolArch+ - Parameter Files and Settings
File Locations
After having completed the MolArch+ installations and settings you will find the following parameter files on your systems in the directory indicated by the environment variable $MOLARCH.
  • In the $MOLARCH directory all parameter definition files are found, which are used by MolArch+ and its various sub-systems. These include for example atom and bond parameters, color definitions, crystallographic spacegroup descriptions, help and syntax descriptions, and descriptions of the command lines used to call external programs such as a VRML viewer or POVRAY.
  • $MOLARCH/backgrounds and $MOLARCH/logos: Files used by animation scripts to render video frames.
  • $MOLARCH/examples: Example files (gzipped format) illustrating the use of MolArch+. MolArch+ is able to read gzipped files by temporarily unzipping them in the current working directory if you have appropriate write permissions.
  • $MOLARCH/examples/images: Collection of molecular images contained in the "molecular graphics" section of this web-site.
  • $MOLARCH/examples/movies: Collection of script-files (tar-archives) and images used to create the animations contained in the "molecular movies" section of this web-site.
  • $MOLARCH/scripts: Collection of shell scripts and small programs files that may be used to manipulate images and create animations. These files and binaries may be copied to a local directory contained in your $PATH variable if needed.
Global Settings
In general, all global (for all users) settings of MolArch+ are taken from the files contained in the $MOLARCH directory. All parameter files are ASCII formatted files (human readable). Unless invoked with the '-s' option, MolArch+ prints messages on the console whenever it has used such a file:
        LOAD KEYS   $MOLARCH/molarch+.key
        LOAD COL    COLORS     8      INDEX   0 -   7      $MOLARCH/colorstd.par
        LOAD APAR   NPAR     119      $MOLARCH/atoms.par
All global settings may be replaced by user-edited local parameter files (see below).
Local Settings
Local (for individual users) settings of MolArch+ may be made by copying the corresponding global parameter file to a private directory and editing the file. Each parameter file is searched by MolArch+ (in that order) at the following locations: working directory, home directory ($HOME), and installation ($MOLARCH) directory. Visible files supersede hidden files (filenames starting with '.'). Whatever file is found first will be used by MolArch+. If crucial files are not found at any location, MolArch+ may abort immediately or with a short error message only.

For example, the file "atoms.par" (which contains atom specific parameters used by MolArch+) will be searched (in that order) at the following locations:

  • ./atoms.par
  • ./.atoms.par
  • $HOME/atoms.par
  • $HOME/.atoms.par
  • $MOLARCH/atoms.par
  • $MOLARCH/.atoms.par
Copy and edit the files to fit your needs, but remember that parameter files in $HOME will affect all your invocations of MolArch+, while those contained in the working directory will only affect those started from a command line from this directory. Missing files, wrong file formats, and unexpected changes to the formatted ASCII files may abort MolArch+ without warning.

A short description on some of the parameter files is given below.

Top of Page MolArch+ - Parameter File Descriptions
Short messages (usage or syntax) displayed by the various the programs "<file>" when invoked with the '-h' (help) option (e.g. file "molarch+.use").
Detailed description (help file) for some programs "<file>".
MolArch+ settings of display parameters which are read at program start-up. Copy this file to your home directory and edit as needed.
MolArch+ help and syntax descriptions. These files contain a detailed description of all MolArch+ commands available, as well as a short syntax notation for quick reference. You definitely should have a look at these files. The MolArch+ 'help', 'syntax', and 'apropos' commands display selected parts of these files.
This file is used by the MolArch+ syntax checker if the option 'set syntax-check on' is set. Use with caution as it may not be fully up-to-date.
MolArch+ key short-cut definitions.
As the MolArch+ doesn't understand window resizing, the preferred main window's dimensions may be specified here.
MolArch+ script file which may contain default set-up statements to be executed automatically at each program start. The graphics version of MolArch+ (molarch+) will first look for a file "molarch+.spr", then for "molarch-.spr" and will execute whatever file is found first; the non-graphics version (molarch-) prefers the settings contained in "molarch-.spr". This may be used to configure both program versions differently.
Basically identical to the above "molarch+.spr" and "molarch-.spr" script files, but executed first. As an exception, the names of these set-up files must start with '.', un-hidden (visible) files are not used.
Atomic parameters. May not need editing unless you want to change the atomic radius for bond-calculations (column "VDWR") or display (column ATSLD).
Bond parameters for calculating bond orders of multiple bonds.
Default parameters for calculating hydrogen-bonds. These values may be re-defined from the MolArch+ command line.
Default parameters for calculating J3H-H and J3C-H coupling constants.
Ring geometry parameters for calculating the Cremer-Pople ring puckering parameters of five- and six-membered rings.
Advanced fragment definitions used for the calculation of molecular connectivity indices for QSAR studies.
MolArch+ color scale definitions to be used with the 'cmap' command.
MolArch+ space group definitions used for handling crystal structure files.
Advanced fragment definitions used to create solid shapes for the display of inorganic solid-state structures and crystal packings. These files are used by the MolArch+ 'make solid ...' commands.
Advanced definitions for schematic atomic orbital representations.
Top of Page MolArch+ - Parameter Files for External Viewers
This file contains the command line used by MolArch+ to call an external VRML viewer. Edit this file to fit your needs.
This file contains the command line used by MolArch+ to call the external ray-tracing program POVRAY. Edit this file to fit your needs.
POVRAY default color and camera definitions used by MolArch+. Make sure that the location of these files is specified in the POVRAY Library_Path for include files. You may have to edit your local "~/.povrayrc" file to include the $MOLARCH installation directory.

© Copyright PD Dr. S. Immel