usage: ample [-h] [-ROSETTA ROSETTA_path] [-RDB ROSETTA_database]
             [-fragsexe path to make_fragments.pl]
             [-Rosetta_cluster path to Rosettas cluster] [-fasta fasta_file]
             [-name priotein name] [-NProc NoProcessors]
             [-RunDir run_directory] [-SCWRL path to scwrl]
             [-LGA path_to_LGA dir] [-MAX Maxcluster exe]
             [-THESEUS Theseus exe required] [-MTZ MTZ in]
             [-MODELS folder of decoys] [-MakeModels Do the modelling]
             [-ROSETTA_DIR Rosetta_dir] [-make_frags bool to make fragments]
             [-3mers 3mers] [-9mers 9mers] [-F flag for F]
             [-SIGF flag for SIGF] [-FREE flag for FREE]
             [-CLUSTER using a cluster]

Structure solution by abinitio modeling

optional arguments:
  -h, --help            show this help message and exit
  -ROSETTA ROSETTA_path
                        path for Rosetta AbinitioRelax
  -RDB ROSETTA_database
                        path for Rosetta database
  -fragsexe path to make_fragments.pl
                        location of make_fragments.pl
  -Rosetta_cluster path to Rosettas cluster
                        location of rosetta cluster
  -fasta fasta_file     protein fasta file. (required)
  -name priotein name   name of protien in the format ABCD
  -NProc NoProcessors   number of processers (default 1)
  -RunDir run_directory
                        directory to put files (default current dir)
  -SCWRL path to scwrl  pathway to SCWRL exe
  -LGA path_to_LGA dir  pathway to LGA folder (not the exe) will use the 'lga'
                        executable
  -MAX Maxcluster exe   Maxcluster exe
  -THESEUS Theseus exe (required)
                        Theseus exe
  -MTZ MTZ in           MTZ in
  -MODELS folder of decoys
                        folder of decoys
  -MakeModels Do the modelling
                        run rosetta modeling, set to False to import pre-made
                        models (required if making models locally default
                        True)
  -ROSETTA_DIR Rosetta_dir
                        the Rosetta install directory
  -make_frags bool to make fragments
                        Bool, True to make non homologous framents, False to
                        import fragments
  -3mers 3mers          path of imported 3mers
  -9mers 9mers          path of imported 9mers
  -F flag for F         Flag for F
  -SIGF flag for SIGF   Flag for SIGF
  -FREE flag for FREE   Flag for FREE
  -CLUSTER using a cluster
                        will submit jobs to a cluster





Requirements: 
needs some 3rd party software:
Maxcluster
Rosetta
Theseus
SQWRL

Known Issues:
1) it is recommended to use -OLD_shelx False for use on clusters
2)assumes that the number of models to make is > number of processors 
3)Theseus is also known to hang if not compiled (will be caught and rerun until success)
4)needs a long command line (might need to increase command line length)
5)shelx will infiniate loop if space group is P -1  this is changed to P1