domainsse1
Add secondary structure records to a dcf file.
Usage
domainsse -dcfinfile
infile
-dccfdir
directory
-dcfoutfile
outfile
-logfile
outfile
domainsse -help
Overview
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