To run analyze enter the command:

analyze-clust infile angfile [outfile]
(all functions but NMR fitting)

or

analyze-morass infile angfile [outfile] [noefile]
(NMR fitting, but no minimum-variance clustering)

The third argument is optional.

where:

infile.inp contains main data.

outo.angfile contains the EDMC outo.* file to be processed

outfile.out will contain the list file

outfile.ang will contain the dihedral angles of the leading families if
         cluster analysis is carried out.

noefile.noe contains experimental NOE intensities.

If the third argument is missing, it is set at angfile. If the fourth 
argument is missing, it is set at infile.

The output files will contain the following:

outfile.out - list file

outfile.ang - the dihedral angles of the leading families, if cluster 
      analysis is carried out.

outfile.tex - if minimal-tree clustering is carried out, it will contain
      the LaTeX picture output of the graph representing the minimal spanning
      tree. 

outfile.noe_out - calculated NOE intensities for each conformation, if 
      requested so (analyze-morass only). This output is created only, if 
      no NMR fitting, but only calculation of NOE intensities was requested.

outfile.coupl_out - calculated coupling constants for each conformation, if
      requested so (analyze-morass only). This output is created only, if 
      no NMR fitting, but only calculation of coupling constants was requested.