MATGEN3D documentation |
Generates a 3D-1D scoring matrix from CCF files (clean coordinate files).
ID D1CS4A_ XX EN 1CS4 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Adenylyl and guanylyl cyclase catalytic domain XX FA Adenylyl and guanylyl cyclase catalytic domain XX DO Adenylyl cyclase VC1, domain C1a XX OS Dog (Canis familiaris) XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // |
SUMiNijArr A 0 B 0 C 0 D 10 E 0 F 4 G 5 H 0 I 5 J 6 K 0 L 6 M 12 N 0 O 6 P 14 Q 0 R 8 S 4 T 0 U 9 NiArr A 10 B 0 C 3 D 6 E 11 F 7 G 4 H 3 I 7 J 0 K 4 L 11 M 1 N 4 O 0 P 1 Q 5 R 3 S 2 T 3 U 0 V 3 W 0 X 0 Y 1 [Part of this file has been deleted for brevity] B 0.000 C 0.034 D 0.067 E 0.124 F 0.079 G 0.045 H 0.034 I 0.079 J 0.000 K 0.045 L 0.124 M 0.011 N 0.045 O 0.000 P 0.011 Q 0.056 R 0.034 S 0.022 T 0.034 U 0.000 V 0.034 W 0.000 X 0.000 Y 0.011 Z 0.000 |
D1CS4A_ R:D-2 S:C A:63.80 OEnv AO:D R:I-3 S:T A:28.30 OEnv AF:I R:E-4 S:T A:113.00 OEnv AU:E R:G-5 S:T A:104.20 OEnv AU:G R:F-6 S:H A:23.70 OEnv AD:F R:T-7 S:H A:111.60 OEnv AS:T R:S-8 S:H A:84.60 OEnv AP:S R:L-9 S:H A:57.60 OEnv AJ:L R:A-10 S:H A:24.00 OEnv AD:A R:S-11 S:T A:78.20 OEnv AR:S R:Q-12 S:T A:78.00 OEnv AR:Q R:C-13 S:T A:28.80 OEnv AF:C R:T-14 S:C A:72.00 OEnv AO:T R:A-15 S:H A:103.00 OEnv AS:A R:Q-16 S:H A:88.10 OEnv AP:Q R:E-17 S:H A:66.30 OEnv AM:E R:L-18 S:H A:17.70 OEnv AD:L R:V-19 S:H A:79.50 OEnv AP:V R:M-20 S:H A:78.40 OEnv AP:M R:T-21 S:H A:74.90 OEnv AM:T R:L-22 S:H A:16.50 OEnv AD:L R:N-23 S:H A:94.00 OEnv AS:N R:E-24 S:H A:74.00 OEnv AM:E R:L-25 S:H A:40.60 OEnv AG:L [Part of this file has been deleted for brevity] OEnv AD:F R:A-26 S:H A:59.60 OEnv AJ:A R:E-27 S:H A:62.30 OEnv AM:E R:A-28 S:H A:76.30 OEnv AP:A R:F-29 S:H A:20.30 OEnv AD:F R:K-30 S:H A:64.60 OEnv AM:K R:N-31 S:H A:68.30 OEnv AM:N R:A-32 S:H A:71.80 OEnv AM:A R:L-33 S:H A:42.20 OEnv AG:L R:E-34 S:H A:56.50 OEnv AJ:E R:I-35 S:H A:70.20 OEnv AM:I R:A-36 S:H A:27.70 OEnv AD:A R:V-37 S:H A:89.80 OEnv AP:V R:Q-38 S:H A:80.20 OEnv AP:Q R:E-39 S:H A:73.50 OEnv AM:E R:N-40 S:C A:109.90 OEnv AU:N R:V-41 S:C A:44.50 OEnv AI:V R:D-42 S:C A:105.60 OEnv AU:D R:F-43 S:C A:83.50 OEnv AR:F R:I-44 S:C A:43.50 OEnv AI:I R:L-45 S:C A:87.00 OEnv AR:L R:I-46 S:C A:30.40 OEnv AI:I R:A-47 S:C A:108.40 OEnv AU:A R:G-48 S:C A:102.60 OEnv AU:G R:D-49 S:C A:72.50 OEnv AO:D R:L-50 S:C A:55.40 OEnv AL:L |
# 3D-1D Scoring matrix created by matgen3d # ajResidueEnv1 # Total SCOP entries: 2 # No. of files opened: 2 # No. of files not opened: 0 A R N D C Q E G H I L K M F P S T W Y V B Z X * AA 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AB 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AC 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AD 0.98 1.09 0.80 0.39 1.09 0.58 -0.21 0.80 1.09 0.24 0.48 0.80 2.19 1.63 2.19 1.49 1.09 -2.30 2.19 1.09 -2.30 -2.30 -2.30 -2.64 AE 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AF 0.80 2.00 1.72 1.31 2.00 1.49 0.70 1.72 2.00 1.85 0.70 1.72 3.10 1.16 3.10 2.41 2.00 -1.39 3.10 2.00 -1.39 -1.39 -1.39 -2.64 AG 0.58 1.78 1.49 1.09 1.78 1.27 0.48 1.49 1.78 0.93 1.17 1.49 2.88 0.93 2.88 2.19 1.78 -1.61 2.88 1.78 -1.61 -1.61 -1.61 -2.64 AH 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AI 0.58 1.78 1.49 1.09 1.78 1.27 0.48 1.49 1.78 2.03 0.48 1.49 2.88 0.93 2.88 2.19 1.78 -1.61 2.88 1.78 -1.61 -1.61 -1.61 -2.64 AJ 1.09 1.60 1.31 0.91 1.60 1.09 0.99 1.31 1.60 0.75 0.30 1.31 2.70 0.75 2.70 2.00 1.60 -1.79 2.70 1.60 -1.79 -1.79 -1.79 -2.64 AK 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AL 0.39 1.60 1.31 0.91 1.60 1.09 0.30 1.31 1.60 0.75 0.30 1.31 2.70 0.75 2.70 2.00 1.60 -1.79 2.70 1.60 -1.79 -1.79 -1.79 -2.64 AM -0.30 0.91 0.62 0.21 0.91 0.39 0.99 0.62 0.91 0.06 -0.39 0.62 2.00 0.06 2.00 1.31 0.91 -2.48 2.00 0.91 -2.48 -2.48 -2.48 -2.64 AN 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AO 0.39 1.60 1.31 1.60 1.60 1.09 0.30 1.31 1.60 0.75 0.30 1.31 2.70 0.75 2.70 2.00 1.60 -1.79 2.70 1.60 -1.79 -1.79 -1.79 -2.64 AP 0.24 0.75 0.46 0.06 0.75 1.34 0.14 0.46 0.75 -0.10 -0.55 0.46 1.85 -0.10 1.85 1.16 0.75 -2.64 1.85 1.44 -2.64 -2.64 -2.64 -2.64 AQ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AR 0.11 1.31 1.02 0.62 1.31 0.80 0.01 1.02 1.31 0.46 0.01 1.02 2.41 0.46 2.41 1.72 1.31 -2.08 2.41 1.31 -2.08 -2.08 -2.08 -2.64 AS 0.80 2.00 1.72 1.31 2.00 1.49 0.70 1.72 2.00 1.16 0.70 1.72 3.10 1.16 3.10 2.41 2.00 -1.39 3.10 2.00 -1.39 -1.39 -1.39 -2.64 AT 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -2.64 AU -0.01 1.19 0.91 0.50 1.19 0.68 -0.11 2.00 1.19 0.35 -0.11 0.91 2.29 0.35 2.29 1.60 1.19 -2.20 2.29 1.19 -2.20 -2.20 -2.20 -2.64 * -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 |
Generate a 3D-1D scoring matrix from CCF files. Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): -mode menu [1] This option specifies the amino acid residue positions to use in calculating the substitution data. (Values: 1 (All amino acid positions for domains in a DCF file); 2 (Ligand-binding positions.)) * -model menu [1] This option specifies whether to use all ligands or a specific set of ligands present in a CON file when calculating the substitution data. (Values: 1 (All ligands within a CON file); 2 (Select ligands within a CON file.)) * -dcfinfile infile This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. * -coninfile infile This option specifies the location of CON files (contact files) (output). 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. * -liginfile infile This option specifies the location of the ligand list file. This file contains a list of ligand ('heterogen') 3-character identifier codes. One id code should be given per line. [-ccfddir] directory [./] This option specifies the location of CCF files (clean coordinate files) (input) which have been processed by using PDBPLUS. 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. * -ccfpdir directory [./] This option specifies the location of CCF files (clean coordinate files) (input) which have been processed by using PDBPLUS. 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. -modee 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)) [-scmatrixfile] outfile [matgen3d.out] Domainatrix substitution matrix output file [-calclogfile] outfile [matgen3d.calc] Domainatrix calculations log output file [-logfile] outfile [matgen3d.log] Domainatrix log output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-ccfddir" associated qualifiers -extension1 string Default file extension "-ccfpdir" associated qualifiers -extension string Default file extension "-scmatrixfile" associated qualifiers -odirectory2 string Output directory "-calclogfile" associated qualifiers -odirectory3 string Output directory "-logfile" associated qualifiers -odirectory4 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 | ||||||||||||||||||||||||||||||||||||
-mode | list | This option specifies the amino acid residue positions to use in calculating the substitution data. |
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1 | ||||||||||||||||||||||||||||||||
-model | list | This option specifies whether to use all ligands or a specific set of ligands present in a CON file when calculating the substitution data. |
|
1 | ||||||||||||||||||||||||||||||||
-dcfinfile | infile | This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. | Input file | Required | ||||||||||||||||||||||||||||||||
-coninfile | infile | This option specifies the location of CON files (contact files) (output). 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 | ||||||||||||||||||||||||||||||||
-liginfile | infile | This option specifies the location of the ligand list file. This file contains a list of ligand ('heterogen') 3-character identifier codes. One id code should be given per line. | Input file | Required | ||||||||||||||||||||||||||||||||
[-ccfddir] (Parameter 1) |
directory | This option specifies the location of CCF files (clean coordinate files) (input) which have been processed by using PDBPLUS. 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. | Directory | ./ | ||||||||||||||||||||||||||||||||
-ccfpdir | directory | This option specifies the location of CCF files (clean coordinate files) (input) which have been processed by using PDBPLUS. 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. | Directory | ./ | ||||||||||||||||||||||||||||||||
-modee | list | This option specifies the environment definition. See matgen3d documentation for description of definitions. |
|
1 | ||||||||||||||||||||||||||||||||
[-scmatrixfile] (Parameter 2) |
outfile | Domainatrix substitution matrix output file | Output file | matgen3d.out | ||||||||||||||||||||||||||||||||
[-calclogfile] (Parameter 3) |
outfile | Domainatrix calculations log output file | Output file | matgen3d.calc | ||||||||||||||||||||||||||||||||
[-logfile] (Parameter 4) |
outfile | Domainatrix log output file | Output file | matgen3d.log | ||||||||||||||||||||||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||
(none) | ||||||||||||||||||||||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||
(none) | ||||||||||||||||||||||||||||||||||||
Associated qualifiers | ||||||||||||||||||||||||||||||||||||
"-ccfddir" associated directory qualifiers | ||||||||||||||||||||||||||||||||||||
-extension1 -extension_ccfddir |
string | Default file extension | Any string | ccf | ||||||||||||||||||||||||||||||||
"-ccfpdir" associated directory qualifiers | ||||||||||||||||||||||||||||||||||||
-extension | string | Default file extension | Any string | ccf | ||||||||||||||||||||||||||||||||
"-scmatrixfile" associated outfile qualifiers | ||||||||||||||||||||||||||||||||||||
-odirectory2 -odirectory_scmatrixfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||
"-calclogfile" associated outfile qualifiers | ||||||||||||||||||||||||||||||||||||
-odirectory3 -odirectory_calclogfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||
"-logfile" associated outfile qualifiers | ||||||||||||||||||||||||||||||||||||
-odirectory4 -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 |
% matgen3d Generate a 3D-1D scoring matrix from CCF files. DCF file amino acid positions 1 : All amino acid positions for domains in a DCF file 2 : Ligand-binding positions. This option specifies the amino acid residue positions to use in calculating the substitution data. [1]: 1 Domain classification file (optional): ../scopparse-keep/all.scop Clean domain coordinates directory [./]: ../domainer-keep Choose environment definition. 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 This option specifies the environment definition. See matgen3d documentation for description of definitions. [1]: 1 Domainatrix substitution matrix output file [matgen3d.out]: Domainatrix calculations log output file [matgen3d.calc]: Domainatrix log output file [matgen3d.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 |
Domain classification file (for SCOP) | DCF format (EMBL-like). | Classification and other data for domains from SCOP. | SCOPPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
Domain classification file (for CATH) | DCF format (EMBL-like). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
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. |
Program name | Description |
---|---|
cathparse | Generates DCF file from raw CATH files |
domainalign | Generate alignments (DAF file) for nodes in a DCF file |
domainnr | Removes redundant domains from a DCF file |
domainrep | Reorder DCF file to identify representative structures |
domainseqs | Adds sequence records to a DCF file |
domainsse | Add secondary structure records to a DCF file |
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
libgen | Generate discriminating elements from alignments |
pepcoil | Predicts coiled coil regions in protein sequences |
rocon | Generates a hits file from comparing two DHF files |
rocplot | Performs ROC analysis on hits files |
scopparse | Generate DCF file from raw SCOP files |
seqalign | Extend alignments (DAF file) with sequences (DHF file) |
seqfraggle | Removes fragment sequences from DHF files |
seqsort | Remove ambiguous classified sequences from DHF files |
seqwords | Generates DHF files from keyword search of UniProt |
ssematch | Search a DCF file for secondary structure matches |
See also http://emboss.sourceforge.net/