#--------------------------------
#Configuration file for PSP tools
#--------------------------------
#-----------------------------------------------------------------------
# Blast parameters
#-----------------------------------------------------------------------
blastdir     /mnt/cfs/pkgs/bhsai/blast-2.2.14
blastdatadir /mnt/cfs/pkgs/bhsai/PSPP/data/blastdb
nrseqdata    /mnt/cfs/pkgs/bhsai/PSPP/data/blastdb/nr
pdbseqdata   /mnt/cfs/pkgs/bhsai/PSPP/data/blastdb/pdbaa
blasttype    pdb             ! Default PSI-BLAST database
psiblastthresh 0.001         ! PSI-BLAST search threshold
psiblastncpus 1
#-----------------------------------------------------------------------
# PPRODO params
#-----------------------------------------------------------------------
pprododir    /mnt/cfs/pkgs/bhsai/PSPP/softwares/pprodo_1.0
boundaryscorethreshold 0.83  ! Threshold for PPRODO program
#-----------------------------------------------------------------------
# PDB directories
#-----------------------------------------------------------------------
pdbdir2      /mnt/cfs/pkgs/bhsai/PSPP/data/pdb/pdb2
pdbdir       /mnt/cfs/pkgs/bhsai/PSPP/data/pdb/data/structures/all/pdb
#-----------------------------------------------------------------------
# PROSPECT params
#-----------------------------------------------------------------------
templatelist   /mnt/cfs/pkgs/bhsai/PSPP/working_templates-1.73.h-95.txt
scoptable      /mnt/cfs/pkgs/bhsai/PSPP/dir_des_scop_txt_1_73.txt
frthresh       8       ! Z-score should be greater than 8 to build model (%50)
maxfr         10       ! Maximum of 10 fold recognition models by default
maxfrsubset  500       ! 100 fold templates to re-score by Z-score
usepsipred     0       ! Use PSIPRED instead of default prospectssp
prospectncpu   1       ! Number of CPUs to use
#-----------------------------------------------------------------------
# Comparative modeling
#-----------------------------------------------------------------------
homthresh        30        ! 30% sequence homology threshold
nestwait         500       ! No. of secs to wait for NEST to complete
allowPDBdownload 1         ! Dont Allow PDB structures to be downloaded from server
maxcm            10        ! Maximum of 10 homology models by default
scorestructs     1         ! Allow running analyze.csh on built models
#-----------------------------------------------------------------------
# Nest command-line options
#-----------------------------------------------------------------------
nestopt          2
nestfast         5
nesttune         3
nestout          0 
#-----------------------------------------------------------------------
# Rosetta params
#-----------------------------------------------------------------------
ainum            5000      ! Number of random models to generate
maxai            5         ! Number of models to do structural FR
scwrlwait        30        ! No. of secs to wait for SCWRL to complete
rosettacmd       -nohoms
#-----------------------------------------------------------------------
