make -k PRED=1a4mA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1a4mA/T0097-1a4mA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a4mA/T0097-1a4mA-2track-local.pw.a2m
make 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1a4mA/T0097-1a4mA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1a4mA/T0097-1a4mA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1aj8A PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1aj8A/T0097-1aj8A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1aj8A/T0097-1aj8A-2track-local.pw.a2m
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1aj8A/T0097-1aj8A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1aj8A/T0097-1aj8A-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1sig PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1sig
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1sig' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1sig/T0097-1sig-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sig/info/1sig.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sig/info/1sig.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sig/info/1sig.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sig/info/1sig.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1sig/T0097-1sig-2track-local.pw.a2m
make 1sig
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1sig' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1sig/T0097-1sig-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sig/info/1sig.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sig/info/1sig.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sig/info/1sig.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sig/info/1sig.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1sig/T0097-1sig-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1quuA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1quuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1quuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1quuA/T0097-1quuA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1quuA/T0097-1quuA-2track-local.pw.a2m
make 1quuA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1quuA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1quuA/T0097-1quuA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1quuA/T0097-1quuA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=2spcA PRED2=2s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 2spcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `2spcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 2spcA/T0097-2spcA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2s/2spcA/info/2spcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2s/2spcA/info/2spcA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2s/2spcA/info/2spcA.stride.seq,/projects/compbio/experiments/models.97/pdb/2s/2spcA/info/2spcA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2spcA/T0097-2spcA-2track-local.pw.a2m
make 2spcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `2spcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 2spcA/T0097-2spcA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2s/2spcA/info/2spcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2s/2spcA/info/2spcA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2s/2spcA/info/2spcA.stride.seq,/projects/compbio/experiments/models.97/pdb/2s/2spcA/info/2spcA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2spcA/T0097-2spcA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1cunA PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1cunA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1cunA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1cunA/T0097-1cunA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cunA/info/1cunA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cunA/info/1cunA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cunA/info/1cunA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cunA/info/1cunA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cunA/T0097-1cunA-2track-local.pw.a2m
make 1cunA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1cunA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1cunA/T0097-1cunA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cunA/info/1cunA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cunA/info/1cunA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cunA/info/1cunA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cunA/info/1cunA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cunA/T0097-1cunA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1ncx  PRED2=1n joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1ncx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1ncx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1ncx/T0097-1ncx-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1ncx/info/1ncx.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ncx/info/1ncx.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1ncx/info/1ncx.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ncx/info/1ncx.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ncx/T0097-1ncx-2track-local.pw.a2m
make 1ncx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1ncx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1ncx/T0097-1ncx-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1ncx/info/1ncx.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ncx/info/1ncx.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1ncx/info/1ncx.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ncx/info/1ncx.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1ncx/T0097-1ncx-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1elrA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1elrA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1elrA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1elrA/T0097-1elrA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1elrA/info/1elrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1elrA/info/1elrA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1elrA/info/1elrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1elrA/info/1elrA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1elrA/T0097-1elrA-2track-local.pw.a2m
make 1elrA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1elrA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1elrA/T0097-1elrA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1elrA/info/1elrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1elrA/info/1elrA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1elrA/info/1elrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1elrA/info/1elrA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1elrA/T0097-1elrA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1qsdA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1qsdA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1qsdA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1qsdA/T0097-1qsdA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qsdA/info/1qsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qsdA/info/1qsdA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qsdA/info/1qsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qsdA/info/1qsdA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qsdA/T0097-1qsdA-2track-local.pw.a2m
make 1qsdA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1qsdA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1qsdA/T0097-1qsdA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qsdA/info/1qsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qsdA/info/1qsdA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qsdA/info/1qsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qsdA/info/1qsdA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qsdA/T0097-1qsdA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1pbwA PRED2=1p joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1pbwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1pbwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1pbwA/T0097-1pbwA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1p/1pbwA/info/1pbwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1p/1pbwA/info/1pbwA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1p/1pbwA/info/1pbwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1p/1pbwA/info/1pbwA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1pbwA/T0097-1pbwA-2track-local.pw.a2m
make 1pbwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1pbwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1pbwA/T0097-1pbwA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1p/1pbwA/info/1pbwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1p/1pbwA/info/1pbwA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1p/1pbwA/info/1pbwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1p/1pbwA/info/1pbwA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1pbwA/T0097-1pbwA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1bpwA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1bpwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1bpwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1bpwA/T0097-1bpwA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bpwA/info/1bpwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bpwA/info/1bpwA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bpwA/info/1bpwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bpwA/info/1bpwA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bpwA/T0097-1bpwA-2track-local.pw.a2m
make 1bpwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1bpwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1bpwA/T0097-1bpwA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bpwA/info/1bpwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bpwA/info/1bpwA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bpwA/info/1bpwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bpwA/info/1bpwA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bpwA/T0097-1bpwA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1qsdA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=2olbA PRED2=2o joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 2olbA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `2olbA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 2olbA/T0097-2olbA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2o/2olbA/info/2olbA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2o/2olbA/info/2olbA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2o/2olbA/info/2olbA.stride.seq,/projects/compbio/experiments/models.97/pdb/2o/2olbA/info/2olbA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2olbA/T0097-2olbA-2track-local.pw.a2m
make 2olbA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `2olbA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 2olbA/T0097-2olbA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2o/2olbA/info/2olbA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2o/2olbA/info/2olbA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2o/2olbA/info/2olbA.stride.seq,/projects/compbio/experiments/models.97/pdb/2o/2olbA/info/2olbA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2olbA/T0097-2olbA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1pbwA PRED2=1p joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make -k PRED=1jevA PRED2=1j joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1jevA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1jevA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1jevA/T0097-1jevA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jevA/info/1jevA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1j/1jevA/info/1jevA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jevA/info/1jevA.stride.seq,/projects/compbio/experiments/models.97/pdb/1j/1jevA/info/1jevA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1jevA/T0097-1jevA-2track-local.pw.a2m
make 1jevA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1jevA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/alpha.new/hmmscore 1jevA/T0097-1jevA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0097.t2k-w0.5.mod,T0097.t2k-2d.mod \
 -db T0097.seq,T0097.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jevA/info/1jevA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1j/1jevA/info/1jevA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jevA/info/1jevA.stride.seq,/projects/compbio/experiments/models.97/pdb/1j/1jevA/info/1jevA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1jevA/T0097-1jevA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'