# - Base directory for creating temporary working directories
#   Replace <user> with your username.
TMPDIR          /scratch/ModPipe/<user>

# - ModPipe results.  
#   Replace <user> with your username.
DATDIR          /netapp/sali/<user>/modpipe_result

# - Template sequence database
TEMPLATESEQDB   /netapp/sali/ModPipe/database/PDB95/db/pdb_95.hdf5

# - PDB repository
PDB_REPOSITORY  /netapp/database/pdb/remediated/uncompressed_files

# - Database of structure profiles
XPRF_LIST	/netapp/sali/ModPipe/database/PDB95/db/pdb95_prf.list
XPRF_PSSMDB	/netapp/sali/ModPipe/database/PDB95/db/pdb95_prf.pssm

# - Non-redundant sequence database (should be in binary form)
NRSEQDB           /netapp/database/uniprot/sequences/uniprot90.hdf5

# -- NCBI Blast database (Specify only the base filename without extension)
#    This will be used to calculate the PSI-Blast profile
NCBISEQDB         /netapp/database/uniprot/sequences/uniprot90

# - Database tag; used to set names for profiles
NRDBTAG           uniprot90

# - TSVMod executables
TSVMODEXE        /netapp/sali/ModPipe/database/TSVMod/programs/main/score_tsvmod.pl

# - Profile update flag
PRFUPDATE         OFF

# - Cutoff value for length of alignments
MINALNLEN         30

# - Number of models per alignment
NUMMODELS         5

# - Scheme to select the best model calculated for each alignment
SELECT_MODEL_BY   DOPEHR
RETURN_MODELS     BEST

# -- Whether to include ligands/waters from the template in the modeling process
HETATOMS          OFF
WATERS            OFF

# -- Parameters for clustering alignments
#    The condition is OVLP > CUT && PCOVLP > CUT && NONOVLP < CUT && 
#    PCNONOVLP < CUT && IDCOL > CUT && PCIDCOL > CUT.
#    -------+++++++++++++
#           +++++++++++++---------
#    The '+' indicates the overlaping region & the '-' indicates
#    the non-overlapping region.
CLUSTERALI                      ON
ALICLUST_OVLP                    0
ALICLUST_PCOVLP                 60
ALICLUST_NONOVLP                20
ALICLUST_PCNONOVLP              20
ALICLUST_IDCOL                   0
ALICLUST_PCIDCOL                80