Lines that should be added Makefile in /projects/compbio/usr/karplus/predict-2nd/testing/training-data.
This is for the first step of  Appendix D.5 Predictability evaluation.

Example:

%.t2k-thin90-CB-burial-14-7: %.ids
        ${PRED-SCRIPTS}/reads-from-ids -a2m t2k-thin90 -2d stride-mixed.CB-burial-14-7 < $^ > $@

New additions:

%.t2k-thin90-near-backbone-7: %.ids
        ${PRED-SCRIPTS}/reads-from-ids -a2m t2k-thin90 -2d stride-mixed.near-backbone-7 < $^ > $@

%.t2k-thin90-near-backbone-11: %.ids
        ${PRED-SCRIPTS}/reads-from-ids -a2m t2k-thin90 -2d stride-mixed.near-backbone-11 < $^ > $@

%.t2k-thin90-way-back-7: %.ids
        ${PRED-SCRIPTS}/reads-from-ids -a2m t2k-thin90 -2d stride-mixed.way-back-7 < $^ > $@

%.t2k-thin90-way-back-11: %.ids
        ${PRED-SCRIPTS}/reads-from-ids -a2m t2k-thin90 -2d stride-mixed.way-back-11 < $^ > $@

After adding these lines to the Makefile then you should execute make. This should produce four files for each 
new alphabet. 

Files created for each alphabet:
dunbrack-in-scop-1.t2k-thin90-ALPHABET-NAME
dunbrack-in-scop-2.t2k-thin90-ALPHABET-NAME
dunbrack-in-scop-3.t2k-thin90-ALPHABET-NAME
t2k-5631.t2k-thin90-ALPHABET-NAME

Next goto directory: /project/compbio/usr/karplus/predict-2nd/testing/burial/run-scripts and
execute the four scripts:

dunbrack-inscop-1+2-IDaahr-5-15-7-15-9-15-13-ALPHABET-NAME-from-empty.script
dunbrack-inscop-1+3-IDaahr-5-15-7-15-9-15-13-ALPHABET-NAME-from-empty.script
dunbrack-inscop-2+3-IDaahr-5-15-7-15-9-15-13-ALPHABET-NAME-from-empty.script
t2k-5631-5-15-7-15-9-15-13-ALPHABET-NAME-from-empty.script

to execute each script use the following command:

/projects/compbio/experiments/models.97/scripts/quick-condor "predict-2nd < SCRIPT >& LOG_FILE" &


First Example:
/projects/compbio/experiments/models.97/scripts/quick-condor "predict-2nd < 
dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.script >& 
dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.log" &