domainssee - Online in the Cloud

PROGRAM:

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

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