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domainssee - Online in the Cloud

Run domainssee in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command domainssee that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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