Fri Apr  4 14:42:43 PDT 2008 Kevin Karplus

This starter directory was copied from
/projects/compbio/experiments/protein-predict/starter-directory-2008/
and will be further modified to improve the protocol for CASP8.





Sun Dec 30 16:41:18 PST 2007 Kevin Karplus

This directory is to contain the new protocol for doing structure predictions.
I'll be starting with the starter-directory-2007 files and rewriting
them, particularly Make.main, which has the guts of the protocol.

Wed May 18 16:26:49 PDT 2005 Kevin Karplus

To make a prediction using the files in this directory, create a new
directory to hold your prediction, and copy Makefile to the new directory.
I recommend creating the directories in
	/projects/compbio/experiments/protein-predict/
for projects that are shared, but this is not essential.

In your new directory, create an a2m file with your target sequence in it.
Note, the a2m format requires that what you want to predict be in uppercase.
For example,

>my_seq	rest of line after space is a comment
ACACACADEDEDEDED

Make the name of the target sequence have only letters, numbers, and underscores.
Use the name of the sequence followed by ".a2m" as the name of the a2m
file ("my_seq.a2m" for the above example).

Edit Makefile to have 
TARGET:= my_seq
instead of 
TARGET:= XXX0000

and do "make -k  >& make.log" on one of the BME linux machines.