EMBOSS: scope

| ## EMBOSS: scope

# Program scope

## Function

Convert raw scop classification file to embl-like format

## Description

Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. A knowledge of these relationships is crucial to our understanding of the evolution of proteins and of development. It will also play an important role in the analysis of the sequence data that is being produced by worldwide genome projects.

The SCOP database aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known, including all entries in the Protein Data Bank (PDB).

scope reads the SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?dir=lin

scope writes the SCOP classification to an EMBL-like format file.

No changes are made to the data other than changing the format in which it is held.

This EMBL-like format SCOP file is used by several other EMBOSS programs.

The reason why the SCOP database format is changed to an EMBL-like format before being used used by other EMBOSS programs is that it is an easier format to work with than the native SCOP database format.

## Usage

Here is a sample session with scope:

    % scope
    Convert raw scop classification file to embl-like format
    Name of scop file for input (raw format) [scop.orig]: /data/scop/scop.orig
    Name of scop file for output (embl-like format) [Escop.dat]: Escop.test

## Command line arguments

       Mandatory qualifiers:
      [-infile]            infile     Name of scop file for input (raw format)
      [-outfile]           outfile    Name of scop file for output (embl-like
                                      format)

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | Name of scop file for input (raw format) | Input file | scop.orig
[-outfile] (Parameter 2) | Name of scop file for output (embl-like format) | Output file | Escop.dat
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

The native format SCOP database input file is available at http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?dir=lin

The format of this file is explained at http://scop.mrc-lmb.cam.ac.uk/scop/parindex.html

The file given at this URL contains a single line for each domain in SCOP, including text describing the position of the domain in the SCOP hierarchy. Note that other SCOP classification files, without this annotation, are available at http://scop.mrc-lmb.cam.ac.uk/scop/parindex.html

## Output file format

The output records used to describe an entry are given below. Records (4) to (8) are used to describe the position of the domain in the scop hierarchy.

1. ID - Domain identifier code. This is a 7-character code that uniquely identifies the domain in scop. It is identical to the first 7 characters of a line in the scop classification file. The first character is always 'D', the next four characters are the PDB identifier code, the fifth character is the PDB chain identifier to which the domain belongs (a '.' is given in cases where the domain is composed of multiple chains, a '_' is given where a chain identifier was not specified in the PDB file) and the final character is the number of the domain in the chain (for chains comprising more than one domain) or '_' (the chain comprises a single domain only).
2. EN - PDB identifier code. This is the 4-character PDB identifier code of the PDB entry containing the domain.
3. OS - Source of the protein. It is identical to the text given after 'Species' in the scop classification file.
4. CL - Domain class. It is identical to the text given after 'Class' in the scop classification file.
5. FO - Domain fold. It is identical to the text given after 'Fold' in the scop classification file.
6. SF - Domain superfamily. It is identical to the text given after 'Superfamily' in the scop classification file.
7. FA - Domain family. It is identical to the text given after 'Family' in the scop classification file.
8. DO - Domain name. It is identical to the text given after 'Protein' in the scop classification file.
9. NC - Number of chains comprising the domain (usually 1). If the number of chains is greater than 1, then the domain entry will have a section containing a CN and a CH record (see below) for each chain.
10. CN - Chain number. The number given in brackets after this record indicates the start of the data for the relevent chain.
11. CH - Domain definition. The character given before CHAIN is the PDB chain identifier (a '.' is given in cases where a chain identifier was not specified in the scop classification file), the strings before START and END give the start and end positions respectively of the domain in the PDB file (a '.' is given in cases where a position was not specified). Note that the start and end positions refer to residue numbering given in the original pdb file and therefore must be treated as strings.

An example of an excerpt from an output file follows:

    ID   D3SDHA_
    XX
    EN   3SDH
    XX
    OS   Ark clam (Scapharca inaequivalvis)
    XX
    CL   All alpha proteins
    XX
    FO   Globin-like
    XX
    SF   Globin-like
    XX
    FA   Globins
    XX
    DO   Hemoglobin I
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   a CHAIN; . START; . END;
    //
    ID   D3SDHB_
    XX
    EN   3SDH
    XX
    OS   Ark clam (Scapharca inaequivalvis)
    XX
    CL   All alpha proteins
    XX
    FO   Globin-like
    XX
    SF   Globin-like
    XX
    FA   Globins
    XX
    DO   Hemoglobin I
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   b CHAIN; . START; . END;
    //

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cutgextract | Extract data from CUTG
domainer | Build domain coordinate files
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one
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 classifications file and writes embl-like format scop classification file
seqnr | Converts redundant database results to a non-redundant set of hits
tfextract | Extract data from TRANSFAC

## Author(s)

This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)

## History

Written (Jan 2001) - Jon Ison.

## Target users

This program is intended to be run by EMBOSS site maintainers or those responsible for setting up and maintaining protein 3D structural data for use by others.

## Comments