make -k PRED=1pedA PRED2=1p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make 1pedA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1pedA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1pedA/T0112-1pedA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1p/1pedA/info/1pedA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1p/1pedA/info/1pedA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1p/1pedA/info/1pedA.stride.seq,/projects/compbio/experiments/models.97/pdb/1p/1pedA/info/1pedA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1pedA/T0112-1pedA-2track-local.pw.a2m make 1pedA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1pedA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1pedA/T0112-1pedA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1p/1pedA/info/1pedA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1p/1pedA/info/1pedA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1p/1pedA/info/1pedA.stride.seq,/projects/compbio/experiments/models.97/pdb/1p/1pedA/info/1pedA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1pedA/T0112-1pedA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' make -k PRED=1ykfA PRED2=1y joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make 1ykfA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1ykfA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1ykfA/T0112-1ykfA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1y/1ykfA/info/1ykfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1y/1ykfA/info/1ykfA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1y/1ykfA/info/1ykfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1y/1ykfA/info/1ykfA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ykfA/T0112-1ykfA-2track-local.pw.a2m make 1ykfA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1ykfA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1ykfA/T0112-1ykfA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1y/1ykfA/info/1ykfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1y/1ykfA/info/1ykfA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1y/1ykfA/info/1ykfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1y/1ykfA/info/1ykfA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ykfA/T0112-1ykfA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' make -k PRED=2ohxA PRED2=2o joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' mkdir 2ohxA fixmode 2ohxA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/T0112-2ohxA-local.pw -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/T0112-2ohxA-local.pw.a2m make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `2ohxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/2ohxA-T0112-local.pw -i /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/2ohxA-T0112-local.pw.a2m make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `2ohxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/T0112-2ohxA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq,/projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/T0112-2ohxA-2track-local.pw.a2m make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `2ohxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/T0112-2ohxA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq,/projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/T0112-2ohxA-2track-global.pw.a2m make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `2ohxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/T0112-2ohxA-vit.pw \ -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/T0112-2ohxA-vit.pw.a2m make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `2ohxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/2ohxA-T0112-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/2ohxA-T0112-vit.pw.a2m make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `2ohxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/T0112-2ohxA-global.pw -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/T0112-2ohxA-global.pw.a2m make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `2ohxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/2ohxA-T0112-global.pw -i /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/2ohxA-T0112-global.pw.a2m make 2ohxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `2ohxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 2ohxA/2ohxA-T0112-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2o/2ohxA/struct-align/2ohxA.fssp-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2ohxA/2ohxA-T0112-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' make -k PRED=1agnA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make 1agnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' mkdir 1agnA fixmode 1agnA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1agnA/T0112-1agnA-local.pw -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1agnA/T0112-1agnA-local.pw.a2m make 1agnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1agnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1agnA/1agnA-T0112-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1agnA/nostruct-align/1agnA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1agnA/1agnA-T0112-local.pw.a2m make 1agnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1agnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1agnA/T0112-1agnA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1agnA/T0112-1agnA-2track-local.pw.a2m make 1agnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1agnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1agnA/T0112-1agnA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1agnA/T0112-1agnA-2track-global.pw.a2m make 1agnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1agnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1agnA/T0112-1agnA-vit.pw \ -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1agnA/T0112-1agnA-vit.pw.a2m make 1agnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1agnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1agnA/1agnA-T0112-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1agnA/nostruct-align/1agnA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1agnA/1agnA-T0112-vit.pw.a2m make 1agnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1agnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1agnA/T0112-1agnA-global.pw -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1agnA/T0112-1agnA-global.pw.a2m make 1agnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1agnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1agnA/1agnA-T0112-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1agnA/nostruct-align/1agnA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1agnA/info/1agnA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1agnA/1agnA-T0112-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' make -k PRED=1qorA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' mkdir 1qorA fixmode 1qorA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/T0112-1qorA-local.pw -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/T0112-1qorA-local.pw.a2m make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1qorA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/1qorA-T0112-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qorA/nostruct-align/1qorA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/1qorA-T0112-local.pw.a2m make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1qorA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/T0112-1qorA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/T0112-1qorA-2track-local.pw.a2m make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1qorA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/T0112-1qorA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0112.t2k-w0.5.mod,T0112.t2k-2d.mod \ -db T0112.seq,T0112.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/T0112-1qorA-2track-global.pw.a2m make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1qorA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/T0112-1qorA-vit.pw \ -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/T0112-1qorA-vit.pw.a2m make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1qorA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/1qorA-T0112-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1q/1qorA/nostruct-align/1qorA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/1qorA-T0112-vit.pw.a2m make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1qorA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/T0112-1qorA-global.pw -i T0112.t2k-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/T0112-1qorA-global.pw.a2m make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1qorA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/1qorA-T0112-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qorA/nostruct-align/1qorA.t99-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/1qorA-T0112-global.pw.a2m make 1qorA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t112' make[2]: `1qorA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t112' /projects/compbio/bin/alpha.new/hmmscore 1qorA/1qorA-T0112-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qorA/struct-align/1qorA.fssp-w0.5.mod -db T0112.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qorA/info/1qorA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qorA/1qorA-T0112-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t112'