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; // |
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 SE EEEEEEE XX SS SEQUENCE 189 AA; 24290 MW; D1929097 CRC32; LLLLLLLEEE EEEEEEEEEE ELHHHHHHHL LHHHHHHHHH HHHHHHHHHH HHHHLLEEEE EELLEEEEEE LLLLLLLHHH HHHHHHHHHH HHHHHHHHHH HHLLLLEEEE EEEEEEEEEL LLLLLLLLEE EHHHHHHHHH HHHHLLLLLE EEEHHHHHLL LLLLLEEELH HHHHHHHHHH HLLLEEEEL 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 SE HEEE XX SS SEQUENCE 43 AA; 5411 MW; 61C5458D CRC32; LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // |
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Standard (Mandatory) qualifiers: [-dcfinfile] infile This option specifies the name of the 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. [-dccfdir] directory This option specifies the location of the domain 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. [-dcfoutfile] outfile This option specifies the name of the DCF file (domain classification file) with secondary structure records (output). 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. [-errfile] outfile This option specifies the name of the DOMAINSSE log file. Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-dcfoutfile" associated qualifiers -odirectory3 string Output directory "-errfile" associated qualifiers -odirectory4 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write 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. 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 deaths
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-dcfinfile] (Parameter 1) |
This option specifies the name of the 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 |
[-dccfdir] (Parameter 2) |
This option specifies the location of the domain 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. | Directory | ./ |
[-dcfoutfile] (Parameter 3) |
This option specifies the name of the DCF file (domain classification file) with secondary structure records (output). 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. | Output file | <sequence>.domainsse |
[-errfile] (Parameter 4) |
This option specifies the name of the DOMAINSSE log file. | Output file | DOMAINSSE.log |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
% domainsse Adds secondary structure records to a DCF file (domain classification file). Name of DCF file (domain classification file) (input): all.scop Location of domain CCF file (clean coordinate file) (input) [./]: Name of DCF file (domain classification file) (output) [all.domainsse]: domainsse.out Name of DOMAINSSE log file. [DOMAINSSE.log]: DOMAINSSE.log Processing D1CS4A_ Processing D1II7A_ Done! output file name: domainsse.out log file name: DOMAINSSE.log |
Go to the input files for this example
Go to the output files for this example
The DCF file (domain classification file) lacking secondary structure information called
/test_data/all.scop was parsed and a DCF file with secondary structure information
called /test_data/domainseqs/all_s.scop was written. Secondary structure information
was taken from CCF files in test_data/.
A log file called /test_data/domainseqs/DOMAINSSE.log was written.
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
Domain classification file (for SCOP) | DCF format (EMBL-like format for domain classification data). | 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 format for domain classification data). | 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 protein) | CCF format (EMBL-like format for protein coordinate and derived data). | Coordinate and other data for a single PDB file. The data are 'cleaned-up': self-consistent and error-corrected. | PDBPARSE | 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 format for protein coordinate and derived data). | Coordinate and other 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 |
---|---|
aaindexextract | Extract data from AAINDEX |
allversusall | Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values |
cathparse | Reads raw CATH classification files and writes DCF file (domain classification file) |
cutgextract | Extract data from CUTG |
domainer | Reads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file) |
domainnr | Removes redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS |
domainseqs | Adds sequence records to a DCF file (domain classification file) |
hetparse | Converts raw dictionary of heterogen groups to a file in EMBL-like format |
pdbparse | Parses PDB files and writes CCF files (clean coordinate files) for proteins |
pdbplus | Add residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain |
pdbtosp | Convert raw swissprot:PDB equivalence file to EMBL-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scopparse | Reads raw SCOP classification files and writes a DCF file (domain classification file) |
seqnr | Removes redundancy from DHF files (domain hits files) or other files of sequences |
sites | Reads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file) |
ssematch | Searches a DCF file (domain classification file) for secondary structure matches |
tfextract | Extract data from TRANSFAC |