make -k PRED=1lea PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1lea/T0096-1lea-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lea/T0096-1lea-2track-local.pw.a2m
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1lea/T0096-1lea-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1lea/T0096-1lea-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make -k PRED=1bia PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1bia/T0096-1bia-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bia/T0096-1bia-2track-local.pw.a2m
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1bia/T0096-1bia-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bia/T0096-1bia-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make -k PRED=2cgpA PRED2=2c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 2cgpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2cgpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2cgpA/T0096-2cgpA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride.seq,/projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cgpA/T0096-2cgpA-2track-local.pw.a2m
make 2cgpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2cgpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2cgpA/T0096-2cgpA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride.seq,/projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cgpA/T0096-2cgpA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make -k PRED=1bi0 PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1bi0/T0096-1bi0-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bi0/T0096-1bi0-2track-local.pw.a2m
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1bi0/T0096-1bi0-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bi0/T0096-1bi0-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make -k PRED=1b78A PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/T0096-1b78A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/T0096-1b78A-2track-local.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/T0096-1b78A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/T0096-1b78A-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make -k PRED=2dtr  PRED2=2d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 2dtr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
mkdir 2dtr
fixmode 2dtr
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2dtr/T0096-2dtr-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2dtr/T0096-2dtr-local.pw.a2m
make 2dtr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2dtr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2dtr/2dtr-T0096-local.pw -i /projects/compbio/experiments/models.97/pdb/2d/2dtr/nostruct-align/2dtr.t99-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2dtr/2dtr-T0096-local.pw.a2m
make 2dtr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2dtr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2dtr/T0096-2dtr-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.seq,/projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2dtr/T0096-2dtr-2track-local.pw.a2m
make 2dtr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2dtr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2dtr/T0096-2dtr-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.seq,/projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2dtr/T0096-2dtr-2track-global.pw.a2m
make 2dtr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2dtr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2dtr/T0096-2dtr-vit.pw \
	-i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2dtr/T0096-2dtr-vit.pw.a2m
make 2dtr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2dtr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2dtr/2dtr-T0096-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/2d/2dtr/nostruct-align/2dtr.t99-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2dtr/2dtr-T0096-vit.pw.a2m
make 2dtr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2dtr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2dtr/T0096-2dtr-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2dtr/T0096-2dtr-global.pw.a2m
make 2dtr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2dtr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 2dtr/2dtr-T0096-global.pw -i /projects/compbio/experiments/models.97/pdb/2d/2dtr/nostruct-align/2dtr.t99-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2d/2dtr/info/2dtr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2dtr/2dtr-T0096-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make -k PRED=1qbjA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
mkdir 1qbjA
fixmode 1qbjA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/T0096-1qbjA-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/T0096-1qbjA-local.pw.a2m
make 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1qbjA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/1qbjA-T0096-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qbjA/nostruct-align/1qbjA.t99-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/1qbjA-T0096-local.pw.a2m
make 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1qbjA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/T0096-1qbjA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/T0096-1qbjA-2track-local.pw.a2m
make 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1qbjA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/T0096-1qbjA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0096.t2k-w0.5.mod,T0096.t2k-2d.mod \
 -db T0096.seq,T0096.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/T0096-1qbjA-2track-global.pw.a2m
make 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1qbjA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/T0096-1qbjA-vit.pw \
	-i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/T0096-1qbjA-vit.pw.a2m
make 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1qbjA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/1qbjA-T0096-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qbjA/nostruct-align/1qbjA.t99-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/1qbjA-T0096-vit.pw.a2m
make 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1qbjA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/T0096-1qbjA-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/T0096-1qbjA-global.pw.a2m
make 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1qbjA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/1qbjA-T0096-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qbjA/nostruct-align/1qbjA.t99-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/1qbjA-T0096-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qbjA/struct-align/1qbjA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qbjA/struct-align/1qbjA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1qbjA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1qbjA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/alpha.new/hmmscore 1qbjA/1qbjA-T0096-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qbjA/struct-align/1qbjA.fssp-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbjA/info/1qbjA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qbjA/1qbjA-T0096-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'