TARGET:= T0468


MANUAL_TOP_HITS ?= \
	1iv7A 1molA 1z02A 2o62A 1k1xA 1nfiE 1nb5I 1fy7A 1a87A \
	1xyiA 2bw2A 1bb8 1c8cA 3bduA 2ra2A 1azpA 2z1cA
	# The first line of templates is from VAST alignments to try2-opt3 < BAKER-ROBETTA_TS5
	# The second line of templates is from best-scores.rdb

REAL_PDB:=2k5wA
include /projects/compbio/experiments/protein-predict/casp8/starter-directory/Make.main


subdomain:
	${STARTER_SCRIPTS}/split-into-domains \
		-first FFF -length LLL \
		-advance  99999 \
		-starter ${STARTER} \
		--nomake < ${TARGET}.a2m


${TARGET}-T0467.a2m: ${TARGET}.t06.w0.5.mod
	${HMMSCORE} ${TARGET}-T0467 \
		-verbose 0 \
		-alphabet protein -i $< -db guide.a2m.gz\
		-db ../T0467/T0467.a2m \
		-db_size ${LIBSIZE} \
		-simple_threshold 10000 \
		-sw 0 -dpstyle 0 -subtract_null 4 \
		-adpstyle 5 \
		-select_align 8

${TARGET}-T0467.str2+nb11.a2m: ${TARGET}.t06-80-60-80-str2+near-backbone-11.mlib
	${HMMSCORE} ${TARGET}-T0467.str2+nb11 \
		-verbose 1 \
		-alphabet protein,protein,str2,near-backbone-11 \
		-trackmod ${TARGET}.t06.w0.5.mod,${TARGET}.t06.w0.5.mod,${TARGET}.t06.str2.mod,${TARGET}.t06.near-backbone-11.mod \
		-trackcoeff 0,0.8,0.6,0.8 \
		-db guide.a2m.gz,guide.a2m.gz,${TARGET}.t06.str2.seq,${TARGET}.t06.near-backbone-11.seq \
		-db ../T0467/guide.a2m.gz,../T0467/guide.a2m.gz,../T0467/T0467.t06.str2.seq,../T0467/T0467.t06.near-backbone-11.seq \
		-db_size ${LIBSIZE} \
		-simple_threshold 1000000 \
		-sw 2 -dpstyle 0 -subtract_null 4 \
		-adpstyle 5 \
		-select_align 8