USAGE
  jiffiloop arguments [input PDB] [output prefix]

  ("jiffiloop" is "java -jar jiffiloop.jar")

ARGUMENTS
  -fragments #                       Limits number of returned fragments.
  -libloc or -librarylocation        Specifies location of fragment parameters 
                                     on local machine. (not really used anymore
                                     with mysql queries, but may be useful for
                                     anyone without access to our mysql
                                     database).
  -pdbloc or -pdblocation            Specifies location of source PDBs on local
                                     machine (important for getting fragments
                                     superimposed on structure).
  -nomatchsize                       Don't match the size of gap.  Useful for
                                     finding fragments which have all same 
                                     parameters except fragment size.
  -ntermsup                          Superimpose fragments with N-terminal
                                     C-alpha on stem's C-alpha.
  -stems or -stem                    Use stem mode (match only one end).
  -norenumber                        Don't renumber the fragments.
  -sequence                          Keep fragment residue identities. Default
                                     is to rename all non-gly, non-pro to ala
                                     and remove sidechains.
  -tighter                           Use tighter parameter ranges (+/- 1 for 
                                     distance, +/- 15 for angles, +/- 10 for 
                                     dihedrals).
  #-#                                Enter integers for the two # signs to
                                     "simulate" a gap to search.
  -distancerange #                   Enter range for distance parameter.
  -angleranges # #                   Enter ranges for two angle parameters.
  -dihedralranges # # #              Enter ranges for three dihedral parameters.
  
