make -k PRED=1hra PRED2=1h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make 1hra
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1hra' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1hra/T0110-1hra-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hra/info/1hra.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hra/info/1hra.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hra/info/1hra.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hra/info/1hra.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1hra/T0110-1hra-2track-local.pw.a2m
make 1hra
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1hra' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1hra/T0110-1hra-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hra/info/1hra.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hra/info/1hra.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hra/info/1hra.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hra/info/1hra.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1hra/T0110-1hra-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
make -k PRED=1lehA PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make 1lehA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
mkdir 1lehA
fixmode 1lehA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1lehA/T0110-1lehA-local.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lehA/T0110-1lehA-local.pw.a2m
make 1lehA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1lehA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1lehA/1lehA-T0110-local.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lehA/nostruct-align/1lehA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lehA/1lehA-T0110-local.pw.a2m
make 1lehA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1lehA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1lehA/T0110-1lehA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lehA/T0110-1lehA-2track-local.pw.a2m
make 1lehA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1lehA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1lehA/T0110-1lehA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lehA/T0110-1lehA-2track-global.pw.a2m
make 1lehA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1lehA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1lehA/T0110-1lehA-vit.pw \
	-i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lehA/T0110-1lehA-vit.pw.a2m
make 1lehA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1lehA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1lehA/1lehA-T0110-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1l/1lehA/nostruct-align/1lehA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lehA/1lehA-T0110-vit.pw.a2m
make 1lehA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1lehA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1lehA/T0110-1lehA-global.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lehA/T0110-1lehA-global.pw.a2m
make 1lehA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1lehA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1lehA/1lehA-T0110-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lehA/nostruct-align/1lehA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lehA/info/1lehA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lehA/1lehA-T0110-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
make -k PRED=1mml  PRED2=1m joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
mkdir 1mml
fixmode 1mml
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/T0110-1mml-local.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/T0110-1mml-local.pw.a2m
make 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1mml' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/1mml-T0110-local.pw -i /projects/compbio/experiments/models.97/pdb/1m/1mml/nostruct-align/1mml.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/1mml-T0110-local.pw.a2m
make 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1mml' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/T0110-1mml-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq,/projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/T0110-1mml-2track-local.pw.a2m
make 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1mml' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/T0110-1mml-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq,/projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/T0110-1mml-2track-global.pw.a2m
make 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1mml' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/T0110-1mml-vit.pw \
	-i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/T0110-1mml-vit.pw.a2m
make 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1mml' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/1mml-T0110-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1m/1mml/nostruct-align/1mml.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/1mml-T0110-vit.pw.a2m
make 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1mml' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/T0110-1mml-global.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/T0110-1mml-global.pw.a2m
make 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1mml' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/1mml-T0110-global.pw -i /projects/compbio/experiments/models.97/pdb/1m/1mml/nostruct-align/1mml.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/1mml-T0110-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1m/1mml/struct-align/1mml.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1m/1mml/struct-align/1mml.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1mml
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1mml' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1mml/1mml-T0110-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1m/1mml/struct-align/1mml.fssp-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mml/info/1mml.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mml/1mml-T0110-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
make -k PRED=1cf9A PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
mkdir 1cf9A
fixmode 1cf9A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0110-1cf9A-local.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0110-1cf9A-local.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/1cf9A-T0110-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cf9A/nostruct-align/1cf9A.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/1cf9A-T0110-local.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0110-1cf9A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0110-1cf9A-2track-local.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0110-1cf9A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0110-1cf9A-2track-global.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0110-1cf9A-vit.pw \
	-i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0110-1cf9A-vit.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/1cf9A-T0110-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1cf9A/nostruct-align/1cf9A.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/1cf9A-T0110-vit.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0110-1cf9A-global.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0110-1cf9A-global.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/1cf9A-T0110-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cf9A/nostruct-align/1cf9A.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/1cf9A-T0110-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1cf9A/struct-align/1cf9A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1cf9A/struct-align/1cf9A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/1cf9A-T0110-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cf9A/struct-align/1cf9A.fssp-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/1cf9A-T0110-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
make -k PRED=1egaA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
mkdir 1egaA
fixmode 1egaA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/T0110-1egaA-local.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/T0110-1egaA-local.pw.a2m
make 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1egaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/1egaA-T0110-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1egaA/nostruct-align/1egaA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/1egaA-T0110-local.pw.a2m
make 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1egaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/T0110-1egaA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/T0110-1egaA-2track-local.pw.a2m
make 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1egaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/T0110-1egaA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/T0110-1egaA-2track-global.pw.a2m
make 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1egaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/T0110-1egaA-vit.pw \
	-i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/T0110-1egaA-vit.pw.a2m
make 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1egaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/1egaA-T0110-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1e/1egaA/nostruct-align/1egaA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/1egaA-T0110-vit.pw.a2m
make 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1egaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/T0110-1egaA-global.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/T0110-1egaA-global.pw.a2m
make 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1egaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/1egaA-T0110-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1egaA/nostruct-align/1egaA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/1egaA-T0110-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1e/1egaA/struct-align/1egaA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1e/1egaA/struct-align/1egaA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1egaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1egaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1egaA/1egaA-T0110-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1egaA/struct-align/1egaA.fssp-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1egaA/info/1egaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1egaA/1egaA-T0110-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
make -k PRED=1otgA PRED2=1o joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
mkdir 1otgA
fixmode 1otgA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/T0110-1otgA-local.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/T0110-1otgA-local.pw.a2m
make 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1otgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/1otgA-T0110-local.pw -i /projects/compbio/experiments/models.97/pdb/1o/1otgA/nostruct-align/1otgA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/1otgA-T0110-local.pw.a2m
make 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1otgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/T0110-1otgA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/T0110-1otgA-2track-local.pw.a2m
make 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1otgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/T0110-1otgA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/T0110-1otgA-2track-global.pw.a2m
make 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1otgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/T0110-1otgA-vit.pw \
	-i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/T0110-1otgA-vit.pw.a2m
make 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1otgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/1otgA-T0110-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1o/1otgA/nostruct-align/1otgA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/1otgA-T0110-vit.pw.a2m
make 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1otgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/T0110-1otgA-global.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/T0110-1otgA-global.pw.a2m
make 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1otgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/1otgA-T0110-global.pw -i /projects/compbio/experiments/models.97/pdb/1o/1otgA/nostruct-align/1otgA.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/1otgA-T0110-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1o/1otgA/struct-align/1otgA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1o/1otgA/struct-align/1otgA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1otgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1otgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1otgA/1otgA-T0110-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1o/1otgA/struct-align/1otgA.fssp-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1otgA/info/1otgA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1otgA/1otgA-T0110-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
make -k PRED=1ek0A PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make 1ek0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
mkdir 1ek0A
fixmode 1ek0A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1ek0A/T0110-1ek0A-local.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ek0A/T0110-1ek0A-local.pw.a2m
make 1ek0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1ek0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1ek0A/1ek0A-T0110-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ek0A/nostruct-align/1ek0A.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ek0A/1ek0A-T0110-local.pw.a2m
make 1ek0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1ek0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1ek0A/T0110-1ek0A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ek0A/T0110-1ek0A-2track-local.pw.a2m
make 1ek0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1ek0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1ek0A/T0110-1ek0A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ek0A/T0110-1ek0A-2track-global.pw.a2m
make 1ek0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1ek0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1ek0A/T0110-1ek0A-vit.pw \
	-i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ek0A/T0110-1ek0A-vit.pw.a2m
make 1ek0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1ek0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1ek0A/1ek0A-T0110-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1e/1ek0A/nostruct-align/1ek0A.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ek0A/1ek0A-T0110-vit.pw.a2m
make 1ek0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1ek0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1ek0A/T0110-1ek0A-global.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ek0A/T0110-1ek0A-global.pw.a2m
make 1ek0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1ek0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1ek0A/1ek0A-T0110-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ek0A/nostruct-align/1ek0A.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ek0A/info/1ek0A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ek0A/1ek0A-T0110-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
make -k PRED=1tsm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make 1tsm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
mkdir 1tsm
fixmode 1tsm
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1tsm/T0110-1tsm-local.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tsm/T0110-1tsm-local.pw.a2m
make 1tsm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1tsm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1tsm/1tsm-T0110-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tsm/nostruct-align/1tsm.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tsm/1tsm-T0110-local.pw.a2m
make 1tsm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1tsm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1tsm/T0110-1tsm-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tsm/T0110-1tsm-2track-local.pw.a2m
make 1tsm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1tsm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1tsm/T0110-1tsm-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0110.t2k-w0.5.mod,T0110.t2k-2d.mod \
 -db T0110.seq,T0110.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tsm/T0110-1tsm-2track-global.pw.a2m
make 1tsm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1tsm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1tsm/T0110-1tsm-vit.pw \
	-i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tsm/T0110-1tsm-vit.pw.a2m
make 1tsm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1tsm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1tsm/1tsm-T0110-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1tsm/nostruct-align/1tsm.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tsm/1tsm-T0110-vit.pw.a2m
make 1tsm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1tsm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1tsm/T0110-1tsm-global.pw -i T0110.t2k-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tsm/T0110-1tsm-global.pw.a2m
make 1tsm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t110'
make[2]: `1tsm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'
/projects/compbio/bin/alpha.new/hmmscore 1tsm/1tsm-T0110-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tsm/nostruct-align/1tsm.t99-w0.5.mod -db T0110.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tsm/info/1tsm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tsm/1tsm-T0110-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t110'