#!/bin/sh
#
set -e

#
#  SCULPTOR:  model editing for MR
#

# run 1 - try to get close to chainsaw options
#         main difference seems to be that it keeps CG1 and CG2 if
#         both available

phaser.sculptor --stdin <<eof
input {
   model {
     file_name = $CEXAM/data/1a80_A.pdb
   }
   alignment {
     file_name = $CEXAM/data/1mzr_1a80.pir
   }
}
output {
  job_title = Chainsaw-like run
  folder = $CCP4_SCR
  root = sculpt_run1
}
macromolecule {
  deletion {
    use = gap
  }
  polishing {
    use = None
  }
  pruning {
    use = schwarzenbacher
  }
  bfactor {
    use = original
  }
  renumber {
    use = target
  }
  rename = True
}
eof

# run 2 - try some different options

phaser.sculptor --stdin <<eof
input {
   model {
     file_name = $CEXAM/data/1a80_A.pdb
   }
   alignment {
     file_name = $CEXAM/data/1mzr_1a80.pir
   }
}
output {
  job_title = second run
  folder = $CCP4_SCR
  root = sculpt_run2
}
macromolecule {
  deletion {
    use = threshold_based_similarity
    threshold_based_similarity {
      threshold = -0.1
    }
  }
  polishing {
    use = remove_short
  }
  pruning {
    use = similarity
  }
  bfactor {
    use = asa
    asa {
      factor = 2
      precision = 960
      probe_radius = 1.4
    }
  }
  renumber {
    use = target
  }
  rename = True
}
eof