domainresoe - Online in the Cloud

PROGRAM:

NAME

domainreso - Remove low resolution domains from a DCF file.

SYNOPSIS

domainreso -cpdbpath dirlist -dcfinfile infile -threshold float -dcfoutfile outfile

domainreso -help

DESCRIPTION

domainreso is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "PROTEIN:3D STRUCTURE" command group(s).

OPTIONS

Input section
-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. Default
value: ./

-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.

Required section
-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. Default
value: 2.8

Output section
-dcfoutfile 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. Default value: test.scop

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