|   | SCOPPARSE documentation | 
| # dir.cla.scop.txt # SCOP release 1.57 (January 2002) [File format version 1.00] # http://scop.mrc-lmb.cam.ac.uk/scop/ # Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html d1cs4a_ 1cs4 A: d.58.29.1 39418 cl=53931,cf=54861,sf=55073,fa=55074,dm=55077,sp=55078,px=39418 d1ii7a_ 1ii7 A: d.159.1.4 62415 cl=53931,cf=56299,sf=56300,fa=64427,dm=64428,sp=64429,px=62415 | 
| # dir.des.scop.txt # SCOP release 1.57 (January 2002) [File format version 1.00] # http://scop.mrc-lmb.cam.ac.uk/scop/ # Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html 53931 cl d - Alpha and beta proteins (a+b) 54861 cf d.58 - Ferredoxin-like 55073 sf d.58.29 - Adenylyl and guanylyl cyclase catalytic domain 55074 fa d.58.29.1 - Adenylyl and guanylyl cyclase catalytic domain 55077 dm d.58.29.1 - Adenylyl cyclase VC1, domain C1a 55078 sp d.58.29.1 - Dog (Canis familiaris) 39418 px d.58.29.1 d1cs4a_ 1cs4 A: 56299 cf d.159 - Metallo-dependent phosphatases 56300 sf d.159.1 - Metallo-dependent phosphatases 64427 fa d.159.1.4 - DNA double-strand break repair nuclease 64428 dm d.159.1.4 - Mre11 64429 sp d.159.1.4 - Archaeon Pyrococcus furiosus 62415 px d.159.1.4 d1ii7a_ 1ii7 A: | 
| 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; // | 
Generate DCF file from raw SCOP files.
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-classfile]         infile     This option specifies the name of raw SCOP
                                  classification file dir.cla.scop.txt_X.XX
                                  (input). This is the raw SCOP classification
                                  file available at
                                  http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57.
  [-desinfile]         infile     This option specifies the name of raw SCOP
                                  description file dir.des.scop.txt_X.XX
                                  (input). This is the raw SCOP description
                                  file available at
                                  http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57.
   -nosegments         boolean    [N] This option specifies whether to omit
                                  domains comprising of more than one segment.
                                  This is necessary if a continuous residue
                                  sequence is required.
   -nomultichain       boolean    [N] This option specifies whether to omit
                                  domains comprising segments from more than
                                  one chain. This is necessary if a continuous
                                  residue sequence is required.
  [-dcffile]           outfile    [test.scop] This option specifies the name
                                  of SCOP DCF file (domain classification
                                  file) (output). A 'domain classification
                                  file' contains classification and other data
                                  for domains from the SCOP or CATH
                                  databases. The file is generated by using
                                  DOMAINER and is in DCF format (EMBL-like).
                                  Domain sequence information can be added to
                                  the file by using DOMAINSEQS.
   Additional (Optional) qualifiers:
   -nominor            boolean    [N] This option specifies whether to omit
                                  domains from minor classes (defined as
                                  anything not in class 'All alpha proteins',
                                  'All beta proteins', 'Alpha and beta
                                  proteins (a/b)' or 'Alpha and beta proteins
                                  (a+b)'). This is necessary or appropriate
                                  for many analyses.
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-dcffile" 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 | ||||
| [-classfile] (Parameter 1) | infile | This option specifies the name of raw SCOP classification file dir.cla.scop.txt_X.XX (input). This is the raw SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57. | Input file | Required | 
| [-desinfile] (Parameter 2) | infile | This option specifies the name of raw SCOP description file dir.des.scop.txt_X.XX (input). This is the raw SCOP description file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57. | Input file | Required | 
| -nosegments | boolean | This option specifies whether to omit domains comprising of more than one segment. This is necessary if a continuous residue sequence is required. | Boolean value Yes/No | No | 
| -nomultichain | boolean | This option specifies whether to omit domains comprising segments from more than one chain. This is necessary if a continuous residue sequence is required. | Boolean value Yes/No | No | 
| [-dcffile] (Parameter 3) | outfile | This option specifies the name of SCOP DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from the SCOP or CATH databases. The file is generated by using DOMAINER and is in DCF format (EMBL-like). Domain sequence information can be added to the file by using DOMAINSEQS. | Output file | test.scop | 
| Additional (Optional) qualifiers | ||||
| -nominor | boolean | This option specifies whether to omit domains from minor classes (defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'). This is necessary or appropriate for many analyses. | Boolean value Yes/No | No | 
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-dcffile" associated outfile qualifiers | ||||
| -odirectory3 -odirectory_dcffile | 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 | 
| % scopparse Generate DCF file from raw SCOP files. Raw scop classification file: scop.cla.raw Raw scop description file: scop.des.raw Omit domains comprising of more than one segment. [N]: Y Omit domains comprising segments from more than one chain. [N]: N Domain classification output file [test.scop]: all.scop | 
Go to the input files for this example
Go to the output files for this example
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO | 
| SCOP parsable files | SCOP format. | Raw SCOP classification data. | Available from http://scop.mrc-lmb.cam.ac.uk/scop/parse/ | N.A. | 
| Domain classification file (for SCOP) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from SCOP. The file is in DCF format (EMBL-like). | SCOPPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. | 
| 
XX
AC   P02213
XX
SP   GLB1_SCAIN
XX
RA   1 START; 146 END;
XX
SQ   SEQUENCE   146 AA;  15947 MW;  5868B4E5 CRC32;
     PSVYDAAAQL TADVKKDLRD SWKVIGSDKK GNGVALMTTL FADNQETIGY FKRLGDVSQG
     MANDKLRGHS ITLMYALQNF IDQLDNPDDL VCVVEKFAVN HITRKISAAE FGKINGPIKK
     VLASKNFGDK YANAWAKLVA VVQAAL
XX
AC   P02213
XX
SP   GLB1_SCAIN
XX
RA   1 START; 146 END; 
XX
SQ   SEQUENCE   146 AA;  15947 MW;  5868B4E5 CRC32;
     PSVYDAAAQL TADVKKDLRD SWKVIGSDKK GNGVALMTTL FADNQETIGY FKRLGDVSQG
     MANDKLRGHS ITLMYALQNF IDQLDNPDDL VCVVEKFAVN HITRKISAAE FGKINGPIKK
     VLASKNFGDK YANAWAKLVA VVQAAL
 | 
| Program name | Description | 
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX | 
| allversusall | Sequence similarity data from all-versus-all comparison | 
| cathparse | Generate DCF file from raw CATH files | 
| cutgextract | Extract codon usage tables from CUTG database | 
| domainalign | Generate alignments (DAF file) for nodes in a DCF file | 
| domainer | Generate domain CCF files from protein CCF files | 
| domainnr | Remove redundant domains from a DCF file | 
| domainrep | Reorder DCF file to identify representative structures | 
| domainseqs | Add sequence records to a DCF file | 
| domainsse | Add secondary structure records to a DCF file | 
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences | 
| hetparse | Convert heterogen group dictionary to EMBL-like format | 
| jaspextract | Extract data from JASPAR | 
| libgen | Generate discriminating elements from alignments | 
| matgen3d | Generate a 3D-1D scoring matrix from CCF files | 
| pdbparse | Parse PDB files and writes protein CCF files | 
| pdbplus | Add accessibility and secondary structure to a CCF file | 
| pdbtosp | Convert swissprot:PDB codes file to EMBL-like format | 
| pepcoil | Predict coiled coil regions in protein sequences | 
| printsextract | Extract data from PRINTS database for use by pscan | 
| prosextract | Process the PROSITE motif database for use by patmatmotifs | 
| rebaseextract | Process the REBASE database for use by restriction enzyme applications | 
| rocon | Generate a hits file from comparing two DHF files | 
| rocplot | Perform ROC analysis on hits files | 
| seqalign | Extend alignments (DAF file) with sequences (DHF file) | 
| seqfraggle | Remove fragment sequences from DHF files | 
| seqnr | Remove redundancy from DHF files | 
| seqsort | Remove ambiguous classified sequences from DHF files | 
| seqwords | Generate DHF files from keyword search of UniProt | 
| sites | Generate residue-ligand CON files from CCF files | 
| ssematch | Search a DCF file for secondary structure matches | 
| tfextract | Process TRANSFAC transcription factor database for use by tfscan | 
See also http://emboss.sourceforge.net/