make -k PRED=1bupA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make 1bupA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
mkdir 1bupA
fixmode 1bupA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1bupA/T0089-1bupA-local.pw -i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bupA/T0089-1bupA-local.pw.a2m
make 1bupA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1bupA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1bupA/1bupA-T0089-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bupA/nostruct-align/1bupA.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bupA/1bupA-T0089-local.pw.a2m
make 1bupA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1bupA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1bupA/T0089-1bupA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0089.t2k-w0.5.mod,T0089.t2k-2d.mod \
 -db T0089.seq,T0089.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bupA/T0089-1bupA-2track-local.pw.a2m
make 1bupA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1bupA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1bupA/T0089-1bupA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0089.t2k-w0.5.mod,T0089.t2k-2d.mod \
 -db T0089.seq,T0089.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bupA/T0089-1bupA-2track-global.pw.a2m
make 1bupA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1bupA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1bupA/T0089-1bupA-vit.pw \
	-i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bupA/T0089-1bupA-vit.pw.a2m
make 1bupA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1bupA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1bupA/1bupA-T0089-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1bupA/nostruct-align/1bupA.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bupA/1bupA-T0089-vit.pw.a2m
make 1bupA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1bupA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1bupA/T0089-1bupA-global.pw -i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bupA/T0089-1bupA-global.pw.a2m
make 1bupA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1bupA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1bupA/1bupA-T0089-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bupA/nostruct-align/1bupA.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bupA/info/1bupA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bupA/1bupA-T0089-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
make -k PRED=1ba1  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
mkdir 1ba1
fixmode 1ba1
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/T0089-1ba1-local.pw -i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/T0089-1ba1-local.pw.a2m
make 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1ba1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/1ba1-T0089-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1ba1/nostruct-align/1ba1.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/1ba1-T0089-local.pw.a2m
make 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1ba1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/T0089-1ba1-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0089.t2k-w0.5.mod,T0089.t2k-2d.mod \
 -db T0089.seq,T0089.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/T0089-1ba1-2track-local.pw.a2m
make 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1ba1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/T0089-1ba1-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0089.t2k-w0.5.mod,T0089.t2k-2d.mod \
 -db T0089.seq,T0089.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/T0089-1ba1-2track-global.pw.a2m
make 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1ba1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/T0089-1ba1-vit.pw \
	-i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/T0089-1ba1-vit.pw.a2m
make 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1ba1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/1ba1-T0089-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1ba1/nostruct-align/1ba1.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/1ba1-T0089-vit.pw.a2m
make 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1ba1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/T0089-1ba1-global.pw -i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/T0089-1ba1-global.pw.a2m
make 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1ba1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/1ba1-T0089-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1ba1/nostruct-align/1ba1.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/1ba1-T0089-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1ba1/struct-align/1ba1.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1ba1/struct-align/1ba1.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1ba1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1ba1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1ba1/1ba1-T0089-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1ba1/struct-align/1ba1.fssp-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1ba1/info/1ba1.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ba1/1ba1-T0089-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
make -k PRED=1kay  PRED2=1k joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make 1kay
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
mkdir 1kay
fixmode 1kay
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1kay/T0089-1kay-local.pw -i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kay/T0089-1kay-local.pw.a2m
make 1kay
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1kay' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1kay/1kay-T0089-local.pw -i /projects/compbio/experiments/models.97/pdb/1k/1kay/nostruct-align/1kay.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kay/1kay-T0089-local.pw.a2m
make 1kay
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1kay' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1kay/T0089-1kay-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0089.t2k-w0.5.mod,T0089.t2k-2d.mod \
 -db T0089.seq,T0089.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kay/T0089-1kay-2track-local.pw.a2m
make 1kay
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1kay' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1kay/T0089-1kay-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0089.t2k-w0.5.mod,T0089.t2k-2d.mod \
 -db T0089.seq,T0089.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kay/T0089-1kay-2track-global.pw.a2m
make 1kay
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1kay' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1kay/T0089-1kay-vit.pw \
	-i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kay/T0089-1kay-vit.pw.a2m
make 1kay
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1kay' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1kay/1kay-T0089-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1k/1kay/nostruct-align/1kay.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kay/1kay-T0089-vit.pw.a2m
make 1kay
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1kay' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1kay/T0089-1kay-global.pw -i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kay/T0089-1kay-global.pw.a2m
make 1kay
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1kay' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1kay/1kay-T0089-global.pw -i /projects/compbio/experiments/models.97/pdb/1k/1kay/nostruct-align/1kay.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kay/info/1kay.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kay/1kay-T0089-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
make -k PRED=1dkgD PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make 1dkgD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
mkdir 1dkgD
fixmode 1dkgD
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1dkgD/T0089-1dkgD-local.pw -i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dkgD/T0089-1dkgD-local.pw.a2m
make 1dkgD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1dkgD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1dkgD/1dkgD-T0089-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dkgD/nostruct-align/1dkgD.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dkgD/1dkgD-T0089-local.pw.a2m
make 1dkgD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1dkgD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1dkgD/T0089-1dkgD-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0089.t2k-w0.5.mod,T0089.t2k-2d.mod \
 -db T0089.seq,T0089.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dkgD/T0089-1dkgD-2track-local.pw.a2m
make 1dkgD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1dkgD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1dkgD/T0089-1dkgD-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0089.t2k-w0.5.mod,T0089.t2k-2d.mod \
 -db T0089.seq,T0089.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dkgD/T0089-1dkgD-2track-global.pw.a2m
make 1dkgD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1dkgD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1dkgD/T0089-1dkgD-vit.pw \
	-i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dkgD/T0089-1dkgD-vit.pw.a2m
make 1dkgD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1dkgD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1dkgD/1dkgD-T0089-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dkgD/nostruct-align/1dkgD.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dkgD/1dkgD-T0089-vit.pw.a2m
make 1dkgD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1dkgD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1dkgD/T0089-1dkgD-global.pw -i T0089.t2k-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dkgD/T0089-1dkgD-global.pw.a2m
make 1dkgD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t89'
make[2]: `1dkgD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'
/projects/compbio/bin/alpha.new/hmmscore 1dkgD/1dkgD-T0089-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dkgD/nostruct-align/1dkgD.t99-w0.5.mod -db T0089.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkgD/info/1dkgD.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dkgD/1dkgD-T0089-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t89'