Starting a new target, say T0240:
	cd ~/casp6
	scripts/new-target T0240
	cd T0240
	(make -k >& make.log; gzip -9f make.log *.atoms) &

Summary of commands to run. Each command should be run from the
target directory unless otherwise noted. I.e.
  
    cd ~/casp6/T0240

Manual try13 run of undertaker (edit try13.under and try13.costfcn):
    /projects/compbio/programs/undertaker/undertaker < try13.under >& try13.log
Manual try13 run, gzip the log
    (/projects/compbio/programs/undertaker/undertaker < try13.under >& try13.log; gzip -9f try13.log) &
Automated try13 run, gzip the log and gzip the pdb outputs
    make decoys/T0240.try13-opt2.pdb.gz

Be sure not to reuse the number (13 in the above example).
The most common error is to neglect to replace all "try13" by "try14"
when editing try14.under which was copied from try13.under.

When editing try2.under from try1.under, comment out the
"PrintTemplateAtoms" command.


Create five model*.ts files for casp (edit model*.method and superimpose-best.under):
    make casp_models

Superimpose several models for easier comparison (edit superimpose-best.under):
    make -k best-models.pdb.gz

Evaluate the models created so far, (nothing to edit)
    make decoys/score-all.try13.pretty
which is like doing these separate steps
    make decoys/score-all.rdb (edit score-all.under to change the costfcn file)
    mv   decoys/score-all.rdb  decoys/score-all.try13.rdb
         prettyscore         < decoys/score-all.try13.rdb > decoys/score-all.try13.pretty
    
Use a version of Rosetta to repack the sidechains of try13-opt2.pdb
    make try13.repack
which does these steps:
    make decoys/T0240.try13-opt2.repack-nonPC.pdb
    make decoys.score-all.try13.rdb

The most common target for a run is (edit try13.under, try13.costfcn):
    make T0240.do13 &
which does these steps:
    make decoys/T0240.try13-opt2.pdb.gz
    make decoys/T0240.try13-opt2.repack-nonPC.pdb
    make decoys.score-all.try13.pretty