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domainsse

NAME

domainsse - Add secondary structure records to a DCF file.

SYNOPSIS

domainsse -dcfinfile infile -dccfdir directory -dcfoutfile outfile -logfile outfile

domainsse -help

DESCRIPTION

domainsse

is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Utils:Database creation" command group(s).

OPTIONS

Input section

-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. Default value: ./

Required section

Advanced section

Output section

-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.

-logfile outfile

This option specifies the name of the DOMAINSSE log file. Default value: domainsse.log

BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

domainsse is fully documented via the tfm(1) system.

AUTHOR

Debian EMBOSS Packaging Team <pkg-emboss-devel@lists.alioth.debian.org>

Wrote the script used to autogenerate this manual page.

COPYRIGHT

Copyright © 2007 Debian EMBOSS Packaging Team

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.