hh-suite/scripts/hhpred/README

How to install hhpred:
======================

1) install the hh-suite library

2) download hhpred databases:
	- hhpred needs hhm, a3m and pdb files for each template, all in the same folder
	- goto http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
	   and download the latest
		pdb70*.a3m.tar.gz, pdb70*.hhm.tar.gz, pdb70*.a3m.tar.gz
	   and extract them into your hhpred database folder
	- enter the path to the database into the config.pm file in the "lib" folder (entry: _pdbdir)
	- enter the path to the uniprot database into the config.pm file in the "lib" folder (entry: _uniprot20)
	- create a folder called "db" in your database folder, open a terminal, change into this folder 
	    and call "cat ../*.hhm > pdb.hhm" 
	
3) install MODELLER
	- enter your MODELLER registration key into the Makefile in "dependencies/Makefile", line 22
	- enter your python version into "dependencies/modeller_cuser/buildall.sh", line 14, (default: 2.7)
	- enter the same python version in the config.pm file in the "lib" folder, lines 44,45 (default: 2.7)
	- make sure you have installed python development files for the specific python version (e.g. python-dev package on ubuntu)
	- execute the Makefile in the dependencies folder (type "make" on a terminal)
	
	
How to run hhpred:
==================

./hhpred.pl -i <infile> -o <outfile>

where <infile> is either a file containing your query sequence (in fasta format)
or a *.a3m file (as generated by e.g. hhblits). When a *.a3m file is given, hhblits will not be called
in the hhpred pipeline.
<outfile> is the resulting pdb file