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DOMAINRESO documentation |
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 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; // |
Standard (Mandatory) qualifiers:
[-cpdbpath] dirlist [./] This option specifies the location of
domain CCF file (clean coordinate files)
(input). A 'clean cordinate file' contains
coordinate and other data for a single PDB
file or a single domain from SCOP or CATH,
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.
[-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.
-threshold float [2.8] This option specifies the threshold
for inclusion (Angstroms). Domains exceeding
the threshold for inclusion (Angstroms)
will not be given in the output file. (Any
numeric value)
[-dcfoutfile] outfile [test.scop] This option specifies the name
of DCF file (domain classification file)
(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.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dcfoutfile" 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. 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
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-cpdbpath] (Parameter 1) |
This option specifies the location of domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, 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 with files | ./ |
| [-dcfinfile] (Parameter 2) |
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 |
| -threshold | This option specifies the threshold for inclusion (Angstroms). Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file. | Any numeric value | 2.8 |
| [-dcfoutfile] (Parameter 3) |
This option specifies the name of DCF file (domain classification file) (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 | test.scop |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
% domainreso Remove low resolution domains from a DCF file. Clean domain coordinates directories [./]: ../domainer-keep/ Domain classification file: ../scopparse-keep/all.scop Threshold for inclusion (Angstroms). [2.8]: 2.3 Domain classification output file [test.scop]: all_2.3.scop /homes/user/test/qa/domainer-keep/d1cs4a_.ccf /homes/user/test/qa/domainer-keep/d1ii7a_.ccf |
Go to the input files for this example
Go to the output files for this example
The following command line would achieve the same result.
domainreso /test_data /test_data/all.scop /test_data/domainreso/all_2.3.scop -threshold 2.3 |
| 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 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 |
|---|---|
| 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 |
| 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 |
| siggenlig | Generates ligand-binding signatures from a CON file |
| sigscan | Generates hits (DHF file) from a signature search |
| sigscanlig | Searches ligand-signature library & writes hits (LHF file) |
See also http://emboss.sourceforge.net/