echo 3.50.3 3.50.3 make -k PRED=1tgoA PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1tgoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1tgoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0109-1tgoA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.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/T0109-1tgoA-2track-local.pw.a2m make 1tgoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1tgoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0109-1tgoA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.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/T0109-1tgoA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make -k PRED=1qqcA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make -k PRED=1d5aA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make -k PRED=1xwl PRED2=1x joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1xwl make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1xwl' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1xwl/T0109-1xwl-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xwl/info/1xwl.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1x/1xwl/info/1xwl.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1x/1xwl/info/1xwl.stride.seq,/projects/compbio/experiments/models.97/pdb/1x/1xwl/info/1xwl.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1xwl/T0109-1xwl-2track-local.pw.a2m make 1xwl make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1xwl' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1xwl/T0109-1xwl-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xwl/info/1xwl.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1x/1xwl/info/1xwl.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1x/1xwl/info/1xwl.stride.seq,/projects/compbio/experiments/models.97/pdb/1x/1xwl/info/1xwl.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1xwl/T0109-1xwl-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.50.1 3.50.1 make -k PRED=1qhaA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1qhaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1qhaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1qhaA/T0109-1qhaA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhaA/info/1qhaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhaA/info/1qhaA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhaA/info/1qhaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhaA/info/1qhaA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qhaA/T0109-1qhaA-2track-local.pw.a2m make 1qhaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1qhaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1qhaA/T0109-1qhaA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhaA/info/1qhaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhaA/info/1qhaA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhaA/info/1qhaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhaA/info/1qhaA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qhaA/T0109-1qhaA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make -k PRED=1dgkN PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1dgkN make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1dgkN' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1dgkN/T0109-1dgkN-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dgkN/info/1dgkN.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dgkN/info/1dgkN.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dgkN/info/1dgkN.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dgkN/info/1dgkN.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dgkN/T0109-1dgkN-2track-local.pw.a2m make 1dgkN make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1dgkN' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1dgkN/T0109-1dgkN-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dgkN/info/1dgkN.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dgkN/info/1dgkN.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dgkN/info/1dgkN.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dgkN/info/1dgkN.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dgkN/T0109-1dgkN-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.19.1 3.19.1 make -k PRED=1qqtA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1qqtA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1qqtA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1qqtA/T0109-1qqtA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qqtA/info/1qqtA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qqtA/info/1qqtA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qqtA/info/1qqtA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qqtA/info/1qqtA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qqtA/T0109-1qqtA-2track-local.pw.a2m make 1qqtA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1qqtA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1qqtA/T0109-1qqtA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qqtA/info/1qqtA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qqtA/info/1qqtA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qqtA/info/1qqtA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qqtA/info/1qqtA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qqtA/T0109-1qqtA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.64.1 3.64.1 make -k PRED=1qj4A PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1qj4A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1qj4A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1qj4A/T0109-1qj4A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qj4A/info/1qj4A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qj4A/info/1qj4A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qj4A/info/1qj4A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qj4A/info/1qj4A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qj4A/T0109-1qj4A-2track-local.pw.a2m make 1qj4A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1qj4A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1qj4A/T0109-1qj4A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qj4A/info/1qj4A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qj4A/info/1qj4A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qj4A/info/1qj4A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qj4A/info/1qj4A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qj4A/T0109-1qj4A-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.1.23 3.1.23 make -k PRED=1pymA PRED2=1p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1pymA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1pymA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1pymA/T0109-1pymA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1p/1pymA/info/1pymA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1p/1pymA/info/1pymA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1p/1pymA/info/1pymA.stride.seq,/projects/compbio/experiments/models.97/pdb/1p/1pymA/info/1pymA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1pymA/T0109-1pymA-2track-local.pw.a2m make 1pymA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1pymA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1pymA/T0109-1pymA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1p/1pymA/info/1pymA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1p/1pymA/info/1pymA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1p/1pymA/info/1pymA.stride.seq,/projects/compbio/experiments/models.97/pdb/1p/1pymA/info/1pymA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1pymA/T0109-1pymA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.55.1 maybe 3.55.1 maybe make -k PRED=1qfxA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1qfxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1qfxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1qfxA/T0109-1qfxA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfxA/info/1qfxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfxA/info/1qfxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfxA/info/1qfxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfxA/info/1qfxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfxA/T0109-1qfxA-2track-local.pw.a2m make 1qfxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1qfxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1qfxA/T0109-1qfxA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfxA/info/1qfxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfxA/info/1qfxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfxA/info/1qfxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfxA/info/1qfxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfxA/T0109-1qfxA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make -k PRED=1bif PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 1bif fixmode 1bif make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/T0109-1bif-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/T0109-1bif-local.pw.a2m make 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bif' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/1bif-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bif/nostruct-align/1bif.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/1bif-T0109-local.pw.a2m make 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bif' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/T0109-1bif-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/T0109-1bif-2track-local.pw.a2m make 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bif' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/T0109-1bif-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/T0109-1bif-2track-global.pw.a2m make 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bif' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/T0109-1bif-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/T0109-1bif-vit.pw.a2m make 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bif' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/1bif-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1bif/nostruct-align/1bif.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/1bif-T0109-vit.pw.a2m make 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bif' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/T0109-1bif-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/T0109-1bif-global.pw.a2m make 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bif' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/1bif-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bif/nostruct-align/1bif.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/1bif-T0109-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bif/struct-align/1bif.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bif/struct-align/1bif.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1bif make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bif' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bif/1bif-T0109-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bif/struct-align/1bif.fssp-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bif/info/1bif.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bif/1bif-T0109-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.18.1 3.18.1 make -k PRED=1cqxA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1cqxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1cqxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1cqxA/T0109-1cqxA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1cqxA/T0109-1cqxA-2track-local.pw.a2m make 1cqxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1cqxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1cqxA/T0109-1cqxA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1cqxA/T0109-1cqxA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.25.1 3.25.1 make -k PRED=2hgsA PRED2=2h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 2hgsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2hgsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2hgsA/T0109-2hgsA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hgsA/info/2hgsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hgsA/info/2hgsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hgsA/info/2hgsA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hgsA/info/2hgsA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2hgsA/T0109-2hgsA-2track-local.pw.a2m make 2hgsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2hgsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2hgsA/T0109-2hgsA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hgsA/info/2hgsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hgsA/info/2hgsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hgsA/info/2hgsA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hgsA/info/2hgsA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2hgsA/T0109-2hgsA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.4.1 3.4.1 make -k PRED=1aa8A PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1aa8A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1aa8A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1aa8A/T0109-1aa8A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aa8A/info/1aa8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aa8A/info/1aa8A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1aa8A/info/1aa8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aa8A/info/1aa8A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1aa8A/T0109-1aa8A-2track-local.pw.a2m make 1aa8A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1aa8A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1aa8A/T0109-1aa8A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aa8A/info/1aa8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aa8A/info/1aa8A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1aa8A/info/1aa8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aa8A/info/1aa8A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1aa8A/T0109-1aa8A-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.2.1 4.140.1 3.2.1 4.140.1 make -k PRED=2cmd PRED2=2c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 2cmd fixmode 2cmd make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/T0109-2cmd-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/T0109-2cmd-local.pw.a2m make 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2cmd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/2cmd-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/2c/2cmd/nostruct-align/2cmd.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/2cmd-T0109-local.pw.a2m make 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2cmd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/T0109-2cmd-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq,/projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/T0109-2cmd-2track-local.pw.a2m make 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2cmd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/T0109-2cmd-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq,/projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/T0109-2cmd-2track-global.pw.a2m make 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2cmd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/T0109-2cmd-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/T0109-2cmd-vit.pw.a2m make 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2cmd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/2cmd-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2c/2cmd/nostruct-align/2cmd.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/2cmd-T0109-vit.pw.a2m make 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2cmd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/T0109-2cmd-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/T0109-2cmd-global.pw.a2m make 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2cmd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/2cmd-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/2c/2cmd/nostruct-align/2cmd.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/2cmd-T0109-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2c/2cmd/struct-align/2cmd.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2c/2cmd/struct-align/2cmd.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 2cmd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `2cmd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 2cmd/2cmd-T0109-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2c/2cmd/struct-align/2cmd.fssp-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2cmd/info/2cmd.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2cmd/2cmd-T0109-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make -k PRED=1bdmA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1bdmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 1bdmA fixmode 1bdmA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bdmA/T0109-1bdmA-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bdmA/T0109-1bdmA-local.pw.a2m make 1bdmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bdmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bdmA/1bdmA-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bdmA/nostruct-align/1bdmA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bdmA/1bdmA-T0109-local.pw.a2m make 1bdmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bdmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bdmA/T0109-1bdmA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bdmA/T0109-1bdmA-2track-local.pw.a2m make 1bdmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bdmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bdmA/T0109-1bdmA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bdmA/T0109-1bdmA-2track-global.pw.a2m make 1bdmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bdmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bdmA/T0109-1bdmA-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bdmA/T0109-1bdmA-vit.pw.a2m make 1bdmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bdmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bdmA/1bdmA-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1bdmA/nostruct-align/1bdmA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bdmA/1bdmA-T0109-vit.pw.a2m make 1bdmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bdmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bdmA/T0109-1bdmA-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bdmA/T0109-1bdmA-global.pw.a2m make 1bdmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bdmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bdmA/1bdmA-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bdmA/nostruct-align/1bdmA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bdmA/info/1bdmA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bdmA/1bdmA-T0109-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make -k PRED=1bmdA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 1bmdA fixmode 1bmdA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/T0109-1bmdA-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/T0109-1bmdA-local.pw.a2m make 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bmdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/1bmdA-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bmdA/nostruct-align/1bmdA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/1bmdA-T0109-local.pw.a2m make 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bmdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/T0109-1bmdA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/T0109-1bmdA-2track-local.pw.a2m make 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bmdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/T0109-1bmdA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/T0109-1bmdA-2track-global.pw.a2m make 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bmdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/T0109-1bmdA-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/T0109-1bmdA-vit.pw.a2m make 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bmdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/1bmdA-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1bmdA/nostruct-align/1bmdA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/1bmdA-T0109-vit.pw.a2m make 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bmdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/T0109-1bmdA-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/T0109-1bmdA-global.pw.a2m make 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bmdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/1bmdA-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bmdA/nostruct-align/1bmdA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/1bmdA-T0109-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bmdA/struct-align/1bmdA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bmdA/struct-align/1bmdA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1bmdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1bmdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1bmdA/1bmdA-T0109-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bmdA/struct-align/1bmdA.fssp-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bmdA/info/1bmdA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bmdA/1bmdA-T0109-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make -k PRED=1ceqA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 1ceqA fixmode 1ceqA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/T0109-1ceqA-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/T0109-1ceqA-local.pw.a2m make 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1ceqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/1ceqA-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1ceqA/nostruct-align/1ceqA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/1ceqA-T0109-local.pw.a2m make 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1ceqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/T0109-1ceqA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/T0109-1ceqA-2track-local.pw.a2m make 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1ceqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/T0109-1ceqA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/T0109-1ceqA-2track-global.pw.a2m make 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1ceqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/T0109-1ceqA-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/T0109-1ceqA-vit.pw.a2m make 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1ceqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/1ceqA-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1ceqA/nostruct-align/1ceqA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/1ceqA-T0109-vit.pw.a2m make 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1ceqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/T0109-1ceqA-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/T0109-1ceqA-global.pw.a2m make 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1ceqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/1ceqA-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1ceqA/nostruct-align/1ceqA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/1ceqA-T0109-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1ceqA/struct-align/1ceqA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1ceqA/struct-align/1ceqA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1ceqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1ceqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1ceqA/1ceqA-T0109-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1ceqA/struct-align/1ceqA.fssp-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ceqA/info/1ceqA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ceqA/1ceqA-T0109-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 1.21.1 4.52.1 1.21.1 4.52.1 make -k PRED=1lbu PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 1lbu fixmode 1lbu make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/T0109-1lbu-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/T0109-1lbu-local.pw.a2m make 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1lbu' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/1lbu-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lbu/nostruct-align/1lbu.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/1lbu-T0109-local.pw.a2m make 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1lbu' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/T0109-1lbu-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/T0109-1lbu-2track-local.pw.a2m make 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1lbu' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/T0109-1lbu-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/T0109-1lbu-2track-global.pw.a2m make 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1lbu' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/T0109-1lbu-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/T0109-1lbu-vit.pw.a2m make 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1lbu' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/1lbu-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1l/1lbu/nostruct-align/1lbu.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/1lbu-T0109-vit.pw.a2m make 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1lbu' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/T0109-1lbu-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/T0109-1lbu-global.pw.a2m make 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1lbu' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/1lbu-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lbu/nostruct-align/1lbu.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/1lbu-T0109-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1l/1lbu/struct-align/1lbu.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1l/1lbu/struct-align/1lbu.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1lbu make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1lbu' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1lbu/1lbu-T0109-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lbu/struct-align/1lbu.fssp-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lbu/info/1lbu.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1lbu/1lbu-T0109-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 4.137.1 4.137.1 make -k PRED=1a6q PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 1a6q fixmode 1a6q make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/T0109-1a6q-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/T0109-1a6q-local.pw.a2m make 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1a6q' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/1a6q-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a6q/nostruct-align/1a6q.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/1a6q-T0109-local.pw.a2m make 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1a6q' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/T0109-1a6q-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/T0109-1a6q-2track-local.pw.a2m make 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1a6q' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/T0109-1a6q-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/T0109-1a6q-2track-global.pw.a2m make 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1a6q' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/T0109-1a6q-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/T0109-1a6q-vit.pw.a2m make 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1a6q' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/1a6q-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1a6q/nostruct-align/1a6q.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/1a6q-T0109-vit.pw.a2m make 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1a6q' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/T0109-1a6q-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/T0109-1a6q-global.pw.a2m make 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1a6q' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/1a6q-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a6q/nostruct-align/1a6q.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/1a6q-T0109-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a6q/struct-align/1a6q.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a6q/struct-align/1a6q.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1a6q make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1a6q' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1a6q/1a6q-T0109-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a6q/struct-align/1a6q.fssp-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6q/info/1a6q.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1a6q/1a6q-T0109-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' echo 3.50.3 3.50.3 make -k PRED=1taq PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1taq make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 1taq fixmode 1taq make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1taq/T0109-1taq-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0109.t2k-w0.5.mod T0109.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -63.945293 Database has 3 sequences with 1821 residues. gzip -f 1taq/T0109-1taq-local.pw.a2m make 1taq make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1taq' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1taq/1taq-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29111/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -477.074310 Database has 3 sequences with 1821 residues. gzip -f 1taq/1taq-T0109-local.pw.a2m make 1taq make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1taq' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1taq/T0109-1taq-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 T0109.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m T0109.t2k-2d.mod(1121): Reading track 1 model from MODEL -- Model from 2nd structure file T0109.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -63.300648 Database has 3 sequences with 1821 residues. gzip -f 1taq/T0109-1taq-2track-local.pw.a2m make 1taq make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1taq' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1taq/T0109-1taq-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0109.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m T0109.t2k-2d.mod(1121): Reading track 1 model from MODEL -- Model from 2nd structure file T0109.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7.024008 Database has 3 sequences with 1821 residues. gzip -f 1taq/T0109-1taq-2track-global.pw.a2m make 1taq make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1taq' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1taq/T0109-1taq-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0109.t2k-w0.5.mod T0109.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -57.761608 Database has 3 sequences with 1821 residues. gzip -f 1taq/T0109-1taq-vit.pw.a2m make 1taq make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1taq' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1taq/1taq-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29111/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -472.911285 Database has 3 sequences with 1821 residues. gzip -f 1taq/1taq-T0109-vit.pw.a2m make 1taq make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1taq' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1taq/T0109-1taq-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0109.t2k-w0.5.mod T0109.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -4.431690 Database has 3 sequences with 1821 residues. gzip -f 1taq/T0109-1taq-global.pw.a2m make 1taq make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1taq' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1taq/1taq-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taq/info/1taq.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1taq/nostruct-align/1taq.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29111/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -468.576019 Database has 3 sequences with 1821 residues. gzip -f 1taq/1taq-T0109-global.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1taq/struct-align/1taq.fssp.a2m.gz', needed by `/projects/compbio/experiments/models.97/pdb/1t/1taq/struct-align/1taq.fssp-w0.5.mod'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taq/xxxx-1taq-T0109-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make: [joints] Error 2 (ignored) make -k PRED=1tgoA PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tgoA/xxxx-1tgoA-T0109-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' make: [joints] Error 2 (ignored) make -k PRED=1hjrA PRED2=1h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make 1hjrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' mkdir 1hjrA fixmode 1hjrA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1hjrA/T0109-1hjrA-local.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0109.t2k-w0.5.mod T0109.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.499588 Database has 3 sequences with 498 residues. gzip -f 1hjrA/T0109-1hjrA-local.pw.a2m make 1hjrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1hjrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1hjrA/1hjrA-T0109-local.pw -i /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4320/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -102.791260 Database has 3 sequences with 498 residues. gzip -f 1hjrA/1hjrA-T0109-local.pw.a2m make 1hjrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1hjrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1hjrA/T0109-1hjrA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 T0109.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m T0109.t2k-2d.mod(1121): Reading track 1 model from MODEL -- Model from 2nd structure file T0109.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.280277 Database has 3 sequences with 498 residues. gzip -f 1hjrA/T0109-1hjrA-2track-local.pw.a2m make 1hjrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1hjrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1hjrA/T0109-1hjrA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0109.t2k-w0.5.mod,T0109.t2k-2d.mod \ -db T0109.seq,T0109.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0109.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m T0109.t2k-2d.mod(1121): Reading track 1 model from MODEL -- Model from 2nd structure file T0109.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -58.804668 Database has 3 sequences with 498 residues. gzip -f 1hjrA/T0109-1hjrA-2track-global.pw.a2m make 1hjrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1hjrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1hjrA/T0109-1hjrA-vit.pw \ -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0109.t2k-w0.5.mod T0109.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.877270 Database has 3 sequences with 498 residues. gzip -f 1hjrA/T0109-1hjrA-vit.pw.a2m make 1hjrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1hjrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1hjrA/1hjrA-T0109-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4320/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -99.184265 Database has 3 sequences with 498 residues. gzip -f 1hjrA/1hjrA-T0109-vit.pw.a2m make 1hjrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1hjrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1hjrA/T0109-1hjrA-global.pw -i T0109.t2k-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0109.t2k-w0.5.mod T0109.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12027/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -51.518673 Database has 3 sequences with 498 residues. gzip -f 1hjrA/T0109-1hjrA-global.pw.a2m make 1hjrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t109' make[2]: `1hjrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t109' /projects/compbio/bin/alpha.new/hmmscore 1hjrA/1hjrA-T0109-global.pw -i /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod -db T0109.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hjrA/info/1hjrA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1h/1hjrA/nostruct-align/1hjrA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4320/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -100.273994 Database has 3 sequences with 498 residues. gzip -f 1hjrA/1hjrA-T0109-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1h/1hjrA/struct-align/1hjrA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1h/1hjrA/struct-align/1hjrA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7788 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7788/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1h/1hjrA/struct-align/1hjrA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1h/1hjrA/struct-align/1hjrA.fssp.a2m.gz (4 sequences, 158 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7788/tmp.a2m. Dropping 3 (of 4) duplicate sequences with differing IDs 1 sequences left after dropping 3 of 4 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7788/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7788/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7788/tmp.a2m (1 sequences, 158 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7788/tmp.mod /projects/compbio/experiments/models.97/pdb/1h/1hjrA/struct-align/1hjrA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7788 80.0% id 3 sequences left after dropping 19 of 22 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31503/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31503/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31503/tmp.a2m (3 sequences, 155 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31503/tmp.mod /projects/compbio/experiments/models.97/pdb/2r/2rn2/struct-align/2rn2.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31503 80.0% id 3 sequences left after dropping 21 of 24 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29168/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29168/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29168/tmp.a2m (3 sequences, 143 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29168/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1b9dA/struct-align/1b9dA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29168 80.0% id 4 sequences left after dropping 2 of 6 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26500/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26500/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26500/tmp.a2m (4 sequences, 295 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26500/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bco/struct-align/1bco.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26500 80.0% id 6 sequences left after dropping 22 of 28 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30797/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30797/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30797/tmp.a2m (6 sequences, 489 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30797/tmp.mod /projects/compbio/experiments/models.97/pdb/1g/1glcG/struct-align/1glcG.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30797 80.0% id 4 sequences left after dropping 5 of 9 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26319/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26319/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26319/tmp.a2m (4 sequences, 862 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26319/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cezA/struct-align/1cezA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26319 80.0% id 2 sequences left after dropping 4 of 6 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30195/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30195/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30195/tmp.a2m (2 sequences, 553 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30195/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1quvA/struct-align/1quvA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30195 80.0% id 4 sequences left after dropping 24 of 28 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16359/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16359/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16359/tmp.a2m (4 sequences, 143 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16359/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cxqA/struct-align/1cxqA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16359