|
|
SIGGENLIG documentation |
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
//
|
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 // |
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 // |
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 // |
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 // |
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 // |
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 // |
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 // |
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 // |
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 // |
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 // |
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 // |
|
|
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
|
| Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||||||
| [-confile] (Parameter 1) |
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. | Input file | Required | ||||||||||||||||||||||||||||||||
| -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: ./ | Directory | |||||||||||||||||||||||||||||||||
| -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: ./ | Directory | |||||||||||||||||||||||||||||||||
| -mode | list | 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. |
|
1 | ||||||||||||||||||||||||||||||||
| -type | list | 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. |
|
1 | ||||||||||||||||||||||||||||||||
| -patchsize | integer | 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 | 5 | ||||||||||||||||||||||||||||||||
| -gapdistance | integer | 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 | 2 | ||||||||||||||||||||||||||||||||
| -environment | list | This option specifies the environment definition. See matgen3d documentation for description of definitions. |
|
1 | ||||||||||||||||||||||||||||||||
| -wsiz | integer | 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 | 0 | ||||||||||||||||||||||||||||||||
| [-sigoutdir] (Parameter 2) |
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. | Output directory | ./ | ||||||||||||||||||||||||||||||||
| [-logfile] (Parameter 3) |
outfile | Domainatrix log output file | Output file | siggenlig.log | ||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||
| (none) | ||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||
| (none) | ||||||||||||||||||||||||||||||||||||
| Associated qualifiers | ||||||||||||||||||||||||||||||||||||
| "-logfile" associated outfile qualifiers | ||||||||||||||||||||||||||||||||||||
| -odirectory3 -odirectory_logfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||
| General qualifiers | ||||||||||||||||||||||||||||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||
% siggenlig
Generates ligand-binding signatures from a CON file
Structure contacts file: ../sites-keep/SITES.con
Clean protein structure coordinates directory (optional) [.]: ../pdbplus-keep
Clean domain coordinates directory (optional) [.]: ../domainer-keep
Available modes
1 : Full-length signature mode
2 : Patch signature mode
Select mode of operation. [1]: 1
Available types
1 : 1D (sequence) signature
2 : 3D (structural) signature
Select type of signature. [1]: 1
Window size [0]:
Domainatrix signature file output directory [./]:
Domainatrix log output file [siggenlig.log]:
|
Go to the input files for this example
Go to the output files for this example
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
| Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
| Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
| Contact file (residue-ligand contacts) | CON format (EMBL-like.) | Residue-ligand contact data for a protein or a domain from SCOP or CATH. | SITES | N.A. |
| Signature file | SIG format | Contains a sparse sequence signature suitable for use with the SIGSCAN program. Contains a sparse sequence signature. | SIGGEN, LIBGEN | The files are generated by using SIGGENLIG. |
| Program name | Description |
|---|---|
| contacts | Generate intra-chain CON files from CCF files |
| domainalign | Generate alignments (DAF file) for nodes in a DCF file |
| domainrep | Reorder DCF file to identify representative structures |
| domainreso | Remove low resolution domains from a DCF file |
| interface | Generate inter-chain CON files from CCF files |
| libgen | Generate discriminating elements from alignments |
| matgen3d | Generate a 3D-1D scoring matrix from CCF files |
| psiphi | Calculates phi and psi torsion angles from protein coordinates |
| rocon | Generates a hits file from comparing two DHF files |
| rocplot | Performs ROC analysis on hits files |
| seqalign | Extend alignments (DAF file) with sequences (DHF file) |
| seqfraggle | Removes fragment sequences from DHF files |
| seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file |
| seqsort | Remove ambiguous classified sequences from DHF files |
| seqwords | Generates DHF files from keyword search of UniProt |
| siggen | Generates a sparse protein signature from an alignment |
| sigscan | Generates hits (DHF file) from a signature search |
| sigscanlig | Searches ligand-signature library & writes hits (LHF file) |
See also http://emboss.sourceforge.net/