echo ReadNeuralNet /projects/compbio/usr/karplus/predict-2nd/testing/networks/overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net > tmp.script
echo ReadA2M T0121.t2k.a2m.gz >> tmp.script
echo PrintPrediction T0121.t2k.2d 3670-4530-6947 >> tmp.script
echo PrintPredictionFasta T0121.t2k.2d.seq >> tmp.script
echo PrintRDB T0121.t2k.2d.rdb >> tmp.script
predict-2nd < tmp.script
# command:# Neural network set to overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net
# command:# Reading A2M format from T0121.t2k.a2m.gz
# Using SequenceWeight EntropyWeight(1.4, 10)
# Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer.
# T0121.t2k.a2m with 3251 sequences, total weight= 1448.16 avg weight= 0.445449 clipped 46 iterations
# AdjustWeights couldn't save exactly 1.4 bits/position, saving 0.926061 bits.
Regularizing alignment for T0121.t2k.a2m.gz
# After reading T0121.t2k.a2m.gz, have 372 columns in 1 chains
# command:# Initializing Gain for FinalLayer
# Initializing Gain for ordering_layer
# Initializing Gain for SecondLayer
# Initializing Gain for FirstLayer
# Network initialization done
# Printing prediction to T0121.t2k.2d
# command:# Network initialization done
# Printing prediction  in FASTA format to T0121.t2k.2d.seq
# command:# Network initialization done
# Printing prediction to T0121.t2k.2d.rdb
# command:rm tmp.script
/projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0121.t2k.2d.rdb T0121.t2k-2d.mod
/projects/compbio/bin/alpha.new/hmmscore T0121.t2k-2track \
	-trackmod T0121.t2k-w0.5.mod,T0121.t2k-2d.mod \
	-db /projects/compbio/experiments/models.97/indexes/t99.seqs,/projects/compbio/experiments/models.97/indexes/t99.2ds \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -dpstyle 0 \
	-select_score 4 -Emax 40.
SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39
T0121.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6910/tmp.a2m
T0121.t2k-2d.mod(2261):  Reading track 1 model from MODEL -- Model from 2nd structure file T0121.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
....
Average NLL-Simple NULL score:        -15.626302
Database has 3506 sequences with 788879 residues.