/usr/share/doc/ncoils/README is in ncoils 2002-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | /* 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.
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