make -k PRED=1a12A PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a12A/T0088-1a12A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a12A/T0088-1a12A-2track-local.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a12A/T0088-1a12A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a12A/T0088-1a12A-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make -k PRED=1led PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1led/T0088-1led-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1led/T0088-1led-2track-local.pw.a2m
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1led/T0088-1led-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1led/T0088-1led-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make -k PRED=1wkt PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1wkt/T0088-1wkt-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1wkt/T0088-1wkt-2track-local.pw.a2m
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1wkt/T0088-1wkt-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1wkt/T0088-1wkt-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make -k PRED=1amuA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
mkdir 1amuA
fixmode 1amuA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/T0088-1amuA-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/T0088-1amuA-local.pw.a2m
make 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1amuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/1amuA-T0088-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1amuA/nostruct-align/1amuA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/1amuA-T0088-local.pw.a2m
make 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1amuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/T0088-1amuA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/T0088-1amuA-2track-local.pw.a2m
make 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1amuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/T0088-1amuA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/T0088-1amuA-2track-global.pw.a2m
make 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1amuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/T0088-1amuA-vit.pw \
	-i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/T0088-1amuA-vit.pw.a2m
make 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1amuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/1amuA-T0088-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1amuA/nostruct-align/1amuA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/1amuA-T0088-vit.pw.a2m
make 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1amuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/T0088-1amuA-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/T0088-1amuA-global.pw.a2m
make 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1amuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/1amuA-T0088-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1amuA/nostruct-align/1amuA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/1amuA-T0088-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1amuA/struct-align/1amuA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1amuA/struct-align/1amuA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1amuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1amuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1amuA/1amuA-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1amuA/struct-align/1amuA.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1amuA/info/1amuA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1amuA/1amuA-T0088-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make -k PRED=2mprA PRED2=2m joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
mkdir 2mprA
fixmode 2mprA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/T0088-2mprA-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/T0088-2mprA-local.pw.a2m
make 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `2mprA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/2mprA-T0088-local.pw -i /projects/compbio/experiments/models.97/pdb/2m/2mprA/nostruct-align/2mprA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/2mprA-T0088-local.pw.a2m
make 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `2mprA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/T0088-2mprA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq,/projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/T0088-2mprA-2track-local.pw.a2m
make 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `2mprA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/T0088-2mprA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq,/projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/T0088-2mprA-2track-global.pw.a2m
make 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `2mprA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/T0088-2mprA-vit.pw \
	-i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/T0088-2mprA-vit.pw.a2m
make 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `2mprA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/2mprA-T0088-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/2m/2mprA/nostruct-align/2mprA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/2mprA-T0088-vit.pw.a2m
make 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `2mprA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/T0088-2mprA-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/T0088-2mprA-global.pw.a2m
make 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `2mprA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/2mprA-T0088-global.pw -i /projects/compbio/experiments/models.97/pdb/2m/2mprA/nostruct-align/2mprA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/2mprA-T0088-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2m/2mprA/struct-align/2mprA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2m/2mprA/struct-align/2mprA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 2mprA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `2mprA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 2mprA/2mprA-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2m/2mprA/struct-align/2mprA.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2m/2mprA/info/2mprA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2mprA/2mprA-T0088-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
mkdir 1qtsA
fixmode 1qtsA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/T0088-1qtsA-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/T0088-1qtsA-local.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/1qtsA-T0088-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/1qtsA-T0088-local.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/T0088-1qtsA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/T0088-1qtsA-2track-local.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/T0088-1qtsA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/T0088-1qtsA-2track-global.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/T0088-1qtsA-vit.pw \
	-i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/T0088-1qtsA-vit.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/1qtsA-T0088-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/1qtsA-T0088-vit.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/T0088-1qtsA-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/T0088-1qtsA-global.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/1qtsA-T0088-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/1qtsA-T0088-global.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1qtsA/1qtsA-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qtsA/1qtsA-T0088-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make -k PRED=1a1x  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
mkdir 1a1x
fixmode 1a1x
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/T0088-1a1x-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/T0088-1a1x-local.pw.a2m
make 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a1x' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/1a1x-T0088-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a1x/nostruct-align/1a1x.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/1a1x-T0088-local.pw.a2m
make 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a1x' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/T0088-1a1x-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/T0088-1a1x-2track-local.pw.a2m
make 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a1x' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/T0088-1a1x-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0088.t2k-w0.5.mod,T0088.t2k-2d.mod \
 -db T0088.seq,T0088.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/T0088-1a1x-2track-global.pw.a2m
make 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a1x' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/T0088-1a1x-vit.pw \
	-i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/T0088-1a1x-vit.pw.a2m
make 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a1x' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/1a1x-T0088-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1a1x/nostruct-align/1a1x.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/1a1x-T0088-vit.pw.a2m
make 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a1x' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/T0088-1a1x-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/T0088-1a1x-global.pw.a2m
make 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a1x' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/1a1x-T0088-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a1x/nostruct-align/1a1x.t99-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/1a1x-T0088-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a1x/struct-align/1a1x.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a1x/struct-align/1a1x.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1a1x
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a1x' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/alpha.new/hmmscore 1a1x/1a1x-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a1x/struct-align/1a1x.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1x/info/1a1x.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a1x/1a1x-T0088-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'