/* Copyright (c) 2002 Robert B. Russell
 *  EMBL, Meyerhofstrasse 1, 69917 Heidelberg, Germany
 *    Email: russell@embl.de
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA.
 */ 


--- The C program ---
Either re-compile the program as (e.g.)

cc -O2 -I. -o ncoils-osf ncoils.c read_matrix.c -lm

or use the exectuables (ncoils-osf, ncoils-irix) given.

Move the executables to a central bin directory and re-name
as appropriate.

You then need to set an environment variable $COILSDIR to this directory
so that matrices can be seen.

--- An example ---

Seryl tRNA synthetase has two coiled-coil segments, and should be found
by the method.  Try:

ncoils -f < 1srya.fa

You should get:

>1srya SERYL-TRNA SYNTHETASE (E.C.6.1.1.11)  (THERMUS THERMOPHILUS, STRAIN HB27)
MVDLKRLRQEPEVFHRAIREKGVALDLEAxxxxxxxxxxxxxxxxxxxxxxxxxxxxVPK
APPEExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVPLPPWPGAPVGGEEANREI
KRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFM
ARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILP
YEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLE
NAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRA
NLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPC
G
       1 sequences      421 aas       63 in coil                                                                             

Note that the last line "   1 sequences..." is standard error, the rest is
standard out, so if you pipe the output to 1srya_coils.fa you will just
get a BLAST readable file.

--- SERVER ---

coils-svr.pl is a stand alone PERL program that should run the program
in an HTML window if you:

1. Put the program in a /cgi-bin directory
2. Create and make read-writeable by all the directories
  described in the files
3. Have or install the programs "gs" "gnuplot" and "ppmtogif"

I haven't documented this very well, I'm sorry, but I haven't really 
any time.
