RAINBOW(1)

NAME

rainbow - ``rainbow''-color molecule chains

MIDAS COMMAND SYNTAX

Command: rainbow [ modelnumber ... ]

DESCRIPTION

Rainbow colors each chain in the specified model(s) (all models if none specified) from red to blue (transiting through yellow, green, and cyan in the process). This may be of some assistance in tracing tangled molecule chains. Since standard PDB files are ordered from N- to C-terminus, this means that rainbow colors the N-terminus red and the C-terminus blue.

By default rainbow projects its color scheme across the entire model(s) requested, even if parts of those models are not displayed. This is because the rainbow command in MIDAS is an alias that expands to ``pdbrun all nouser rainbow,'' which causes all model information to be sent to rainbow. To restrict the coloring to just the displayed regions, you would have to type ``pdbrun nouser rainbow'' at the MIDAS command prompt.

LIMITATIONS

Rainbow will frequently not work correctly if the device option colormap is ``on'' (from the MIDAS command devopt colormap on). In colormap mode there is only a fixed number of colors available, frequently less than rainbow needs to make a spectrum.

NOTE

Rainbow is a perl script, and as such needs a copy of the perl interpreter in the directory /usr/local/bin. Perl is supplied with all supported platforms of the MidasPlus distribution. However, if you wish to obtain the most recent perl version, the perl distribution can be anonymously ftp'ed from jpl-devvax.jpl.nasa.gov (137.79.113.100), and most likely will be found in the pub/perl.4.0 subdirectory there.

BUGS

The model numbers specified on the rainbow command line cannot be preceded by hash marks (#) as they are in most other MIDAS commands, because the rainbow command is passed through a shell interpreter; the standard shell treats hash marks and anything following hash marks as comments and strips them.

AUTHOR

Eric Pettersen

UCSF Computer Graphics Laboratory