
USAGE
    ramalyze [mode] [infile [outfile]]
    
MODE defaults to '-pdf' but can be any one of the following:

    -pdf        Creates a PDF document that shows all six Ramachandran plots on 
                one page, with outliers labeled and with summary statistics.
                
                For x-ray files with alternate conformations, any residue with
                alternate backbone conformers is analyzed multiple times and 
                counts multiple times in the statistics. All others are analyzed
                once.
                
                For NMR files, the first page will show all model superimposed,
                and subsequent pages show individual models.

    -raw        Analysis is similar to -pdf, but instead of creating a PDF, the 
                following is sent to standard output in colon-delimited format: 
                phi and psi values, Ramachandran evaluation, and category.

    -kinplot    Analysis is similar to -pdf, but the output is a 2D kinemage 
                instead of a PDF.

    -kinmarkup  Outputs 3D kinemage markups centered at the C-alphas of 
                Ramachandran outliers.  If multiple models are present, 
                e.g. in an NMR structure, only the first one is used.
                
    -quiet      Suppresses some command line info output.
    
    [other MODEs may be available in the future]
    
INFILE is a PDB-format file containing one or more models. If it is omitted,
a PDB file will be read from standard input.

OUTFILE is a destination file for the output. It will be overwritten if it
already exists. If OUTFILE is omitted, results will be sent to standard output.

