| ## DOMAINRESO documentation

## CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES

## 1.0 SUMMARY

Remove low resolution domains from a DCF file

## 2.0 INPUTS & OUTPUTS

DOMAINRESO reads a DCF file and writes a DCF file containing the same domains excluding those whose resolution (Angstrom) of structure determination exceeds a user-defined threshold. The resolution data are taken from CCF (clean coordinate files) whose path and file extension (via the ACD file) are specified by the user. The names of the input and output files are also specified by the user.

## 3.0 INPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation.

### Input files for usage example

### File: ../scopparse-keep/all.scop

    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;
    //

## 4.0 OUTPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation.

### Output files for usage example

### File: all_2.3.scop

    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;
    //

## 5.0 DATA FILES

DOMAINRESO does not use any data files.

## 6.0 USAGE

### 6.1 COMMAND LINE ARGUMENTS

    Remove low resolution domains from a DCF file.
    Version: EMBOSS:6.2.0

       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 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
[-cpdbpath] (Parameter 1) | 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. | Directory with files | ./
[-dcfinfile] (Parameter 2) | 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
-threshold | float | 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) | outfile | 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
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dcfoutfile" associated outfile qualifiers
-odirectory3 -odirectory_dcfoutfile | 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

### 6.2 EXAMPLE SESSION

An example of interactive use of DOMAINRESO is shown below. Here is a sample session with domainreso

    % 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

## 7.0 KNOWN BUGS & WARNINGS

No known bugs.

## 8.0 NOTES

Domains that lack a value for resolution in the CCF file (e.g. theoretical models and NMR structures) are included in the output file.

### 8.1 GLOSSARY OF FILE TYPES

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.

None

## 9.0 DESCRIPTION

It is desirable to omit poor resolution protein structures when performing certain analyses of protein domains. DOMAINRESO reads a DCF file (domain classification file) and writes one containing the same domains excluding those whose resolution (Angstrom) of structure determination exceeds a user-defined threshold.

## 10.0 ALGORITHM

None.

## 11.0 RELATED APPLICATIONS

## See also

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)

## 12.0 DIAGNOSTIC ERROR MESSAGES

None.

## 13.0 AUTHORS

Mat Blades (Matthew.Blades@astrazeneca.com)
Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

## 14.0 REFERENCES

Please cite the authors and EMBOSS.
Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

### 14.1 Other useful references