make -k PRED=2reb  PRED2=2r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 2reb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `2reb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 2reb/T0116-2reb-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2r/2reb/info/2reb.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2r/2reb/info/2reb.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2r/2reb/info/2reb.stride.seq,/projects/compbio/experiments/models.97/pdb/2r/2reb/info/2reb.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2reb/T0116-2reb-2track-local.pw.a2m
make 2reb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `2reb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 2reb/T0116-2reb-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2r/2reb/info/2reb.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2r/2reb/info/2reb.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2r/2reb/info/2reb.stride.seq,/projects/compbio/experiments/models.97/pdb/2r/2reb/info/2reb.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2reb/T0116-2reb-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1cr1A PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1cr1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cr1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cr1A/T0116-1cr1A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cr1A/info/1cr1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr1A/info/1cr1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cr1A/info/1cr1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr1A/info/1cr1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cr1A/T0116-1cr1A-2track-local.pw.a2m
make 1cr1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cr1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cr1A/T0116-1cr1A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cr1A/info/1cr1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr1A/info/1cr1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cr1A/info/1cr1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr1A/info/1cr1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cr1A/T0116-1cr1A-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1ng1  PRED2=1n joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1ng1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1ng1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1ng1/T0116-1ng1-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ng1/T0116-1ng1-2track-local.pw.a2m
make 1ng1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1ng1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1ng1/T0116-1ng1-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ng1/T0116-1ng1-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1bkdS PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1bkdS
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1bkdS' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1bkdS/T0116-1bkdS-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bkdS/info/1bkdS.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bkdS/info/1bkdS.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bkdS/info/1bkdS.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bkdS/info/1bkdS.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bkdS/T0116-1bkdS-2track-local.pw.a2m
make 1bkdS
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1bkdS' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1bkdS/T0116-1bkdS-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bkdS/info/1bkdS.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bkdS/info/1bkdS.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bkdS/info/1bkdS.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bkdS/info/1bkdS.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bkdS/T0116-1bkdS-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1b0uA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1b0uA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1b0uA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1b0uA/T0116-1b0uA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b0uA/info/1b0uA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b0uA/info/1b0uA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b0uA/info/1b0uA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b0uA/info/1b0uA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b0uA/T0116-1b0uA-2track-local.pw.a2m
make 1b0uA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1b0uA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1b0uA/T0116-1b0uA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b0uA/info/1b0uA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b0uA/info/1b0uA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b0uA/info/1b0uA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b0uA/info/1b0uA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b0uA/T0116-1b0uA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1shkA PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1shkA/T0116-1shkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1shkA/info/1shkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1shkA/info/1shkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1shkA/info/1shkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1shkA/info/1shkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1shkA/T0116-1shkA-2track-local.pw.a2m
make 1shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1shkA/T0116-1shkA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1shkA/info/1shkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1shkA/info/1shkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1shkA/info/1shkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1shkA/info/1shkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1shkA/T0116-1shkA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=2shkA PRED2=2s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/T0116-2shkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq,/projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2shkA/T0116-2shkA-2track-local.pw.a2m
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/T0116-2shkA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq,/projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2shkA/T0116-2shkA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1qksA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qksA/T0116-1qksA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qksA/T0116-1qksA-2track-local.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qksA/T0116-1qksA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qksA/T0116-1qksA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=6prcL PRED2=6p joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 6prcL
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `6prcL' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 6prcL/T0116-6prcL-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/6p/6prcL/info/6prcL.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/6p/6prcL/info/6prcL.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/6p/6prcL/info/6prcL.stride.seq,/projects/compbio/experiments/models.97/pdb/6p/6prcL/info/6prcL.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 6prcL/T0116-6prcL-2track-local.pw.a2m
make 6prcL
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `6prcL' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 6prcL/T0116-6prcL-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/6p/6prcL/info/6prcL.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/6p/6prcL/info/6prcL.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/6p/6prcL/info/6prcL.stride.seq,/projects/compbio/experiments/models.97/pdb/6p/6prcL/info/6prcL.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 6prcL/T0116-6prcL-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1aijL PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1aijL
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1aijL' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1aijL/T0116-1aijL-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aijL/info/1aijL.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aijL/info/1aijL.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aijL/info/1aijL.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aijL/info/1aijL.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1aijL/T0116-1aijL-2track-local.pw.a2m
make 1aijL
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1aijL' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1aijL/T0116-1aijL-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aijL/info/1aijL.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aijL/info/1aijL.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aijL/info/1aijL.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aijL/info/1aijL.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1aijL/T0116-1aijL-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1tgoA PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
mkdir 1tgoA
fixmode 1tgoA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0116-1tgoA-local.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0116-1tgoA-local.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/1tgoA-T0116-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tgoA/nostruct-align/1tgoA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/1tgoA-T0116-local.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0116-1tgoA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0116-1tgoA-2track-local.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0116-1tgoA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0116-1tgoA-2track-global.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0116-1tgoA-vit.pw \
	-i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0116-1tgoA-vit.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/1tgoA-T0116-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1tgoA/nostruct-align/1tgoA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/1tgoA-T0116-vit.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0116-1tgoA-global.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0116-1tgoA-global.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/1tgoA-T0116-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tgoA/nostruct-align/1tgoA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/1tgoA-T0116-global.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/1tgoA-T0116-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tgoA/struct-align/1tgoA.fssp-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/1tgoA-T0116-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1qlaA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
mkdir 1qlaA
fixmode 1qlaA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/T0116-1qlaA-local.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/T0116-1qlaA-local.pw.a2m
make 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qlaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/1qlaA-T0116-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qlaA/nostruct-align/1qlaA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/1qlaA-T0116-local.pw.a2m
make 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qlaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/T0116-1qlaA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/T0116-1qlaA-2track-local.pw.a2m
make 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qlaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/T0116-1qlaA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/T0116-1qlaA-2track-global.pw.a2m
make 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qlaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/T0116-1qlaA-vit.pw \
	-i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/T0116-1qlaA-vit.pw.a2m
make 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qlaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/1qlaA-T0116-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qlaA/nostruct-align/1qlaA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/1qlaA-T0116-vit.pw.a2m
make 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qlaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/T0116-1qlaA-global.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/T0116-1qlaA-global.pw.a2m
make 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qlaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/1qlaA-T0116-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qlaA/nostruct-align/1qlaA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/1qlaA-T0116-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qlaA/struct-align/1qlaA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qlaA/struct-align/1qlaA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1qlaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1qlaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1qlaA/1qlaA-T0116-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qlaA/struct-align/1qlaA.fssp-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qlaA/info/1qlaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qlaA/1qlaA-T0116-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1cl2A PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
mkdir 1cl2A
fixmode 1cl2A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/T0116-1cl2A-local.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/T0116-1cl2A-local.pw.a2m
make 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl2A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/1cl2A-T0116-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cl2A/nostruct-align/1cl2A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/1cl2A-T0116-local.pw.a2m
make 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl2A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/T0116-1cl2A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/T0116-1cl2A-2track-local.pw.a2m
make 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl2A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/T0116-1cl2A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/T0116-1cl2A-2track-global.pw.a2m
make 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl2A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/T0116-1cl2A-vit.pw \
	-i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/T0116-1cl2A-vit.pw.a2m
make 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl2A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/1cl2A-T0116-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1cl2A/nostruct-align/1cl2A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/1cl2A-T0116-vit.pw.a2m
make 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl2A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/T0116-1cl2A-global.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/T0116-1cl2A-global.pw.a2m
make 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl2A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/1cl2A-T0116-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cl2A/nostruct-align/1cl2A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/1cl2A-T0116-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1cl2A/struct-align/1cl2A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1cl2A/struct-align/1cl2A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1cl2A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl2A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl2A/1cl2A-T0116-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cl2A/struct-align/1cl2A.fssp-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl2A/info/1cl2A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl2A/1cl2A-T0116-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1dg3A PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
mkdir 1dg3A
fixmode 1dg3A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/T0116-1dg3A-local.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/T0116-1dg3A-local.pw.a2m
make 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1dg3A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/1dg3A-T0116-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dg3A/nostruct-align/1dg3A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/1dg3A-T0116-local.pw.a2m
make 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1dg3A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/T0116-1dg3A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/T0116-1dg3A-2track-local.pw.a2m
make 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1dg3A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/T0116-1dg3A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/T0116-1dg3A-2track-global.pw.a2m
make 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1dg3A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/T0116-1dg3A-vit.pw \
	-i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/T0116-1dg3A-vit.pw.a2m
make 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1dg3A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/1dg3A-T0116-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dg3A/nostruct-align/1dg3A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/1dg3A-T0116-vit.pw.a2m
make 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1dg3A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/T0116-1dg3A-global.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/T0116-1dg3A-global.pw.a2m
make 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1dg3A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/1dg3A-T0116-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dg3A/nostruct-align/1dg3A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/1dg3A-T0116-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1d/1dg3A/struct-align/1dg3A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1d/1dg3A/struct-align/1dg3A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1dg3A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1dg3A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1dg3A/1dg3A-T0116-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dg3A/struct-align/1dg3A.fssp-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dg3A/info/1dg3A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dg3A/1dg3A-T0116-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1cl1A PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1cl1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
mkdir 1cl1A
fixmode 1cl1A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl1A/T0116-1cl1A-local.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl1A/T0116-1cl1A-local.pw.a2m
make 1cl1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl1A/1cl1A-T0116-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cl1A/nostruct-align/1cl1A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl1A/1cl1A-T0116-local.pw.a2m
make 1cl1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl1A/T0116-1cl1A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl1A/T0116-1cl1A-2track-local.pw.a2m
make 1cl1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl1A/T0116-1cl1A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl1A/T0116-1cl1A-2track-global.pw.a2m
make 1cl1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl1A/T0116-1cl1A-vit.pw \
	-i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl1A/T0116-1cl1A-vit.pw.a2m
make 1cl1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl1A/1cl1A-T0116-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1cl1A/nostruct-align/1cl1A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl1A/1cl1A-T0116-vit.pw.a2m
make 1cl1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl1A/T0116-1cl1A-global.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl1A/T0116-1cl1A-global.pw.a2m
make 1cl1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1cl1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1cl1A/1cl1A-T0116-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cl1A/nostruct-align/1cl1A.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cl1A/info/1cl1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cl1A/1cl1A-T0116-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
make -k PRED=1clqA PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
mkdir 1clqA
fixmode 1clqA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/T0116-1clqA-local.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/T0116-1clqA-local.pw.a2m
make 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1clqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/1clqA-T0116-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1clqA/nostruct-align/1clqA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/1clqA-T0116-local.pw.a2m
make 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1clqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/T0116-1clqA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/T0116-1clqA-2track-local.pw.a2m
make 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1clqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/T0116-1clqA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0116.t2k-w0.5.mod,T0116.t2k-2d.mod \
 -db T0116.seq,T0116.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/T0116-1clqA-2track-global.pw.a2m
make 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1clqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/T0116-1clqA-vit.pw \
	-i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/T0116-1clqA-vit.pw.a2m
make 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1clqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/1clqA-T0116-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1clqA/nostruct-align/1clqA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/1clqA-T0116-vit.pw.a2m
make 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1clqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/T0116-1clqA-global.pw -i T0116.t2k-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/T0116-1clqA-global.pw.a2m
make 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1clqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/1clqA-T0116-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1clqA/nostruct-align/1clqA.t99-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/1clqA-T0116-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1clqA/struct-align/1clqA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1clqA/struct-align/1clqA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1clqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t116'
make[2]: `1clqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'
/projects/compbio/bin/alpha.new/hmmscore 1clqA/1clqA-T0116-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1clqA/struct-align/1clqA.fssp-w0.5.mod -db T0116.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clqA/info/1clqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1clqA/1clqA-T0116-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t116'