                           SIGGENLIG documentation



CONTENTS

   1.0 SUMMARY
   2.0 INPUTS & OUTPUTS
   3.0 INPUT FILE FORMAT
   4.0 OUTPUT FILE FORMAT
   5.0 DATA FILES
   6.0 USAGE
   7.0 KNOWN BUGS & WARNINGS
   8.0 NOTES
   9.0 DESCRIPTION
   10.0 ALGORITHM
   11.0 RELATED APPLICATIONS
   12.0 DIAGNOSTIC ERROR MESSAGES
   13.0 AUTHORS
   14.0 REFERENCES

1.0 SUMMARY

   Generates ligand-binding signatures from a CON file (contacts file) of
   residue-ligand contacts. Generates ligand-binding signatures from a CON
   file

2.0 INPUTS & OUTPUTS

   SIGGENLIG reads a CON file of residue-ligand contacts generated by
   using SITES and a directory of CCF files (clean coordinate files)
   containing a CCF file for each protein or domain in the CON file. One
   or more signature files, each containing a ligand-binding signature,
   are generated for each ligand-binding site in the CON file. The user
   specifies whether 1D (sequence) or 3D (structural) signatures are
   generated and whether they are 'full-length' (signature corresponds to
   entire ligand-binding site) or 'patch' (signature corresponds to part
   of ligand-binding site). For 3D signatures, the environment definition
   is specified and for patch signatures, a 'Minimum patch size' and
   'Maximum gap distance' are specified. A 'Window size' is specified for
   all signatures. The paths of the CCF files (input) and signature files
   (output) are specified by the user and the file extensions are
   specified in the ACD file. A log file is also written.

3.0 INPUT FILE FORMAT

   The format of the CON file (contacts file) is described in SITES
   documentation. The format of the CCF files is described in PDBPARSE
   documentation (proteins) and the DOMAINER documentation (domains).

  Input files for usage example

  File: ../sites-keep/SITES.con

XX   Residue-ligand contact data (for domains).
XX
TY   LIGAND
XX
EX   THRESH 1.0; IGNORE .; NMOD .; NCHA .;
XX
NE   11
XX
EN   [1]
XX
ID   PDB 1cs4; DOM d1cs4a_; LIG 101;
XX
DE   2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE
XX
SI   SN 1; NS 2
XX
CN   MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 .
XX
S1   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
     ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
XX
NC   SM .; LI 6
XX
LI   ASP 2
LI   PHE 6
LI   THR 7
LI   LEU 44
LI   GLY 45
LI   ASP 46
XX
//
EN   [2]
XX
ID   PDB 1ii7; DOM d1ii7a_; LIG 101;
XX
DE   2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE
XX
SI   SN 2; NS 2
XX
CN   MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 65; NRES2 .
XX
S1   SEQUENCE    65 AA;   7395 MW;  75FBE75B22FD3678 CRC64;
     MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
     LKKAI
XX
NC   SM .; LI 2
XX
LI   HIS 10
LI   ASP 49
XX


  [Part of this file has been deleted for brevity]

NC   SM .; LI 3
XX
LI   ASP 8
LI   HIS 10
LI   ASP 49
XX
//
EN   [10]
XX
ID   PDB 2hhb; DOM .; LIG PO4;
XX
DE   PHOSPHATE ION
XX
SI   SN 1; NS 1
XX
CN   MO .; CN1 1; CN2 .; ID1 D; ID2 .; NRES1 146; NRES2 .
XX
S1   SEQUENCE   146 AA;  15867 MW;  EACBC707CFD466A1 CRC64;
     VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
     KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
     EFTPPVQAAY QKVVAGVANA LAHKYH
XX
NC   SM .; LI 2
XX
LI   VAL 1
LI   LEU 81
XX
//
EN   [11]
XX
ID   PDB 1cs4; DOM d1cs4a_; LIG POP;
XX
DE   PYROPHOSPHATE 2-
XX
SI   SN 1; NS 1
XX
CN   MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 .
XX
S1   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
     ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
XX
NC   SM .; LI 6
XX
LI   ASP 2
LI   ILE 3
LI   GLU 4
LI   GLY 5
LI   PHE 6
LI   THR 7
XX
//

4.0 OUTPUT FILE FORMAT

   The output file (Figure 1) uses the standard signature file format and
   is described in the SIGGEN documentation. For the ligand-binding
   signatures generated by SIGGENLIG, however, four additional lines of
   bibliographic information taken from the CON (input) file are written
   to a signature file. The records have the following meaning:
     * ID - identifier codes: (1) PDB: 4-character PDB identifier code.
       (2) DOM: 7-character domain identifier code from SCOP or CATH. (3)
       LIG: Ligand identifier (an abbreviation of its full name).
     * DE - full name of the ligand, see HETPARSE documentation.
     * IS - ligand-binding site information: (1) SN: Site number. This
       uniquely identifies a ligand-binding site in the CON file generated
       by running SITES. (2) NS: The total number of binding sites for a
       given ligand.
     * IP - path information: (1) PN: Patch number. The sequential order
       (from the N-terminus) of the patch in the ligand-binding site. (2)
       NP: Number of patches. The total number of patches in this
       ligand-binding site. (3) MP: Minimum patch size. (4) MG: Maximum
       gap distance. MP and MG were specified in the generation of the
       signature (see 'Algorithm' below).

   In addition, where 3D signatures are generated, the following records
   have different meanings than for 1D signatures (e.g. those generated by
   using SIGGEN):
     * IN - Informative line about signature position. The number of
       different observed amino acid environments (rather than residue
       identities) is given after 'NRES'
     * AA - The identifier of an environment (rather than residue) seen in
       this position and the frequency of its occurence are delimited by
       ';'.

  Output files for usage example

  File: 101.1.F.#.1cs4.d1cs4a_.sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 1cs4; DOM d1cs4a_; LIG 101;
XX
DE    2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE
XX
IS   SN 1; NS 2
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   6
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
XX
GA   1 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   3 ; 1
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   T ; 1
XX
GA   0 ; 1
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   36 ; 1
XX
NN   [5]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   G ; 1
XX
GA   0 ; 1
XX
NN   [6]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
XX
GA   0 ; 1
//

  File: 101.2.F.#.1ii7.d1ii7a_.sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 1ii7; DOM d1ii7a_; LIG 101;
XX
DE    2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE
XX
IS   SN 2; NS 2
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   2
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   H ; 1
XX
GA   9 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
XX
GA   38 ; 1
//

  File: FOK.1.F.#.1cs4.d1cs4a_.sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 1cs4; DOM d1cs4a_; LIG FOK;
XX
DE    FORSKOLIN
XX
IS   SN 1; NS 1
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   1
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   43 ; 1
//

  File: HEM.1.F.#.2hhb...sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 2hhb; DOM .; LIG HEM;
XX
DE    PROTOPORPHYRIN IX CONTAINING FE
XX
IS   SN 1; NS 4
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   17
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   Y ; 1
XX
GA   41 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   H ; 1
XX
GA   1 ; 1
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [5]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX


  [Part of this file has been deleted for brevity]

XX
GA   0 ; 1
XX
NN   [12]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   3 ; 1
XX
NN   [13]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   V ; 1
XX
GA   1 ; 1
XX
NN   [14]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   N ; 1
XX
GA   3 ; 1
XX
NN   [15]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [16]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   2 ; 1
XX
NN   [17]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   34 ; 1
//

  File: HEM.2.F.#.2hhb...sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 2hhb; DOM .; LIG HEM;
XX
DE    PROTOPORPHYRIN IX CONTAINING FE
XX
IS   SN 2; NS 4
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   17
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   30 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   9 ; 1
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   H ; 1
XX
GA   20 ; 1
XX
NN   [5]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX


  [Part of this file has been deleted for brevity]

XX
GA   0 ; 1
XX
NN   [12]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   3 ; 1
XX
NN   [13]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   V ; 1
XX
GA   1 ; 1
XX
NN   [14]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   N ; 1
XX
GA   3 ; 1
XX
NN   [15]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [16]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   2 ; 1
XX
NN   [17]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   34 ; 1
//

  File: HEM.3.F.#.2hhb...sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 2hhb; DOM .; LIG HEM;
XX
DE    PROTOPORPHYRIN IX CONTAINING FE
XX
IS   SN 3; NS 4
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   19
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   M ; 1
XX
GA   31 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   T ; 1
XX
GA   6 ; 1
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   Y ; 1
XX
GA   2 ; 1
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [5]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX


  [Part of this file has been deleted for brevity]

XX
GA   0 ; 1
XX
NN   [14]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   3 ; 1
XX
NN   [15]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   V ; 1
XX
GA   1 ; 1
XX
NN   [16]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   N ; 1
XX
GA   3 ; 1
XX
NN   [17]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [18]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   2 ; 1
XX
NN   [19]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   34 ; 1
//

  File: HEM.4.F.#.2hhb...sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 2hhb; DOM .; LIG HEM;
XX
DE    PROTOPORPHYRIN IX CONTAINING FE
XX
IS   SN 4; NS 4
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   15
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   30 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   9 ; 1
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   H ; 1
XX
GA   20 ; 1
XX
NN   [5]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX


  [Part of this file has been deleted for brevity]

XX
GA   0 ; 1
XX
NN   [10]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   3 ; 1
XX
NN   [11]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   V ; 1
XX
GA   1 ; 1
XX
NN   [12]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   N ; 1
XX
GA   3 ; 1
XX
NN   [13]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [14]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   2 ; 1
XX
NN   [15]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   34 ; 1
//

  File: MG.1.F.#.1cs4.d1cs4a_.sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 1cs4; DOM d1cs4a_; LIG MG;
XX
DE    MAGNESIUM ION
XX
IS   SN 1; NS 1
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   4
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
XX
GA   1 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   I ; 1
XX
GA   0 ; 1
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   2 ; 1
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
XX
GA   39 ; 1
//

  File: MN.1.F.#.1ii7.d1ii7a_.sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 1ii7; DOM d1ii7a_; LIG MN;
XX
DE    MANGANESE (II) ION
XX
IS   SN 1; NS 1
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   3
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
XX
GA   7 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   H ; 1
XX
GA   1 ; 1
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
XX
GA   38 ; 1
//

  File: PO4.1.F.#.2hhb...sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 2hhb; DOM .; LIG PO4;
XX
DE    PHOSPHATE ION
XX
IS   SN 1; NS 1
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   2
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   V ; 1
XX
GA   0 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 1
XX
GA   79 ; 1
//

  File: POP.1.F.#.1cs4.d1cs4a_.sig

TY   LIGAND
XX
TS   1D
XX
ID   PDB 1cs4; DOM d1cs4a_; LIG POP;
XX
DE    PYROPHOSPHATE 2-
XX
IS   SN 1; NS 1
XX
IP   PN 0; NP 0; MP 5; MG 2
XX
NP   6
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
XX
GA   1 ; 1
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   I ; 1
XX
GA   0 ; 1
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   E ; 1
XX
GA   0 ; 1
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   G ; 1
XX
GA   0 ; 1
XX
NN   [5]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
XX
GA   0 ; 1
XX
NN   [6]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   T ; 1
XX
GA   0 ; 1
//

  File: siggenlig.log


5.0 DATA FILES

   SIGGENLIG does not use any data files.

6.0 USAGE

Generates ligand-binding signatures from a CON file
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-confile]           infile     This option specifies the name of the CON
                                  file (contact file) (input). A 'contact
                                  file' contains contact data for a protein or
                                  a domain from SCOP or CATH, in the CON
                                  format (EMBL-like). The contacts may be
                                  intra-chain residue-residue, inter-chain
                                  residue-residue or residue-ligand. The files
                                  are generated by using CONTACTS, INTERFACE
                                  and SITES.
   -ccfpdir            directory  This option specifies the location of
                                  protein CCF file (clean coordinate files)
                                  (input). A 'clean cordinate file' contains
                                  protein coordinate and derived data for a
                                  single PDB file ('protein clean coordinate
                                  file') or a single domain from SCOP or CATH
                                  ('domain clean coordinate file'), in CCF
                                  format (EMBL-like). The files, generated by
                                  using PDBPARSE (PDB files) or DOMAINER
                                  (domains), contain 'cleaned-up' data that is
                                  self-consistent and error-corrected.
                                  Records for residue solvent accessibility
                                  and secondary structure are added to the
                                  file by using PDBPLUS. default: ./
   -ccfddir            directory  This option specifies the location of
                                  protein CCF file (clean coordinate files)
                                  (input). A 'clean cordinate file' contains
                                  protein coordinate and derived data for a
                                  single PDB file ('protein clean coordinate
                                  file') or a single domain from SCOP or CATH
                                  ('domain clean coordinate file'), in CCF
                                  format (EMBL-like). The files, generated by
                                  using PDBPARSE (PDB files) or DOMAINER
                                  (domains), contain 'cleaned-up' data that is
                                  self-consistent and error-corrected.
                                  Records for residue solvent accessibility
                                  and secondary structure are added to the
                                  file by using PDBPLUS. default: ./
   -mode               menu       [1] This option specifies the mode of
                                  signature generation. In 'Full-length
                                  signature mode' (mode 1) a single signature
                                  incorporating all residue positions that
                                  contact the ligand plus intervening gaps is
                                  generated. In 'Patch signature mode' (mode
                                  2) one or more signatures corresponding to
                                  'patches' of residue positions are
                                  generated. A patch is a set of residues that
                                  are near-neighbours in sequence and is
                                  described by two user-defined parameters:
                                  minimum patch size and maximum gap distance.
                                  (Values: 1 (Full-length signature mode); 2
                                  (Patch signature mode))
   -type               menu       [1] This option specifies the type of
                                  signature generated. In '1D (sequence)
                                  signature' sequence-based signatures are
                                  generated. In '3D (structural) signature'
                                  structure-based signatures are generated.
                                  (Values: 1 (1D (sequence) signature); 2 (3D
                                  (structural) signature))
*  -patchsize          integer    [5] This option specifies the minimum patch
                                  size. This is the minimum number of contact
                                  positions that must be incorporated in a
                                  signature. (Integer 3 or more)
*  -gapdistance        integer    [2] This option specifies the maximum gap
                                  distance. This is the maximum allowable gap
                                  (residues) between two residue in a patch.
                                  If two contact residues are further than
                                  this distance apart in sequence, they would
                                  not belong to the same patch. (Integer 0 or
                                  more)
*  -environment        menu       [1] This option specifies the environment
                                  definition. See matgen3d documentation for
                                  description of definitions. (Values: 1
                                  (Env1); 2 (Env2); 3 (Env3); 4 (Env4); 5
                                  (Env5); 6 (Env6); 7 (Env7); 8 (Env8); 9
                                  (Env9); 10 (Env10); 11 (Env11); 12 (Env12);
                                  13 (Env13); 14 (Env14); 15 (Env15); 16
                                  (Env16))
   -wsiz               integer    [0] This option specifies the window size.
                                  When a signature is aligned to a protein
                                  sequence, the permissible gaps between two
                                  signature positions is determined by the
                                  empirical gaps and the window size. The user
                                  is prompted for a window size that is used
                                  for every position in the signature. Likely
                                  this is not optimal. A future implementation
                                  will provide a range of methods for
                                  generating values of window size depending
                                  upon the alignment (window size is
                                  identified by the WSIZ record in the
                                  signature output file). (Any integer value)
  [-sigoutdir]         outdir     [./] This option specifies the location of
                                  signature files (output). A 'signature file'
                                  contains a sparse sequence signature
                                  suitable for use with the SIGSCAN and
                                  SIGSCANLIG programs. The files are generated
                                  by using SIGGEN and SIGGENLIG.
  [-logfile]           outfile    [siggenlig.log] Domainatrix log output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-logfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


  6.1 COMMAND-LINE ARGUMENTS

