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domainresoe - Online in the Cloud

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This is the command domainresoe 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


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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