make -k 1nseA.indexes \ 1bxm.indexes \ 1au7A.indexes \ 1di2A.indexes \ 1a41.indexes \ 1ebmA.indexes \ 1qgiA.indexes \ 1beo.indexes \ 1unkA.indexes \ 1qpzA.indexes \ 2ezk.indexes make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make -k und/T0098-1nseA-local.index und/1nseA-T0098-local.index \ und/1nseA-T0098-fssp-global.index make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' mkdir tmp mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0098-1nseA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1nseA/T0098-1nseA-local.pw.a2m.gz \ -target T0098 -template 1nseA \ -out T0098-1nseA-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1nseA-orig.a2m Writing a2m file: tmp/1nseA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17428 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17428/tmp -alignfile tmp/1nseA-orig.a2m \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp/1nseA-orig.a2m (1 sequences, 444 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17428/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17428/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17428/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-17428/tmp.a2m (1 sequences, 444 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17428/tmp.mod tmp/1nseA-align.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17428