domainreso1
Remove low resolution domains from a dcf file.
Usage
domainreso -cpdbpath
dirlist
-dcfinfile
infile
-threshold
float
-dcfoutfile
outfile
domainreso -help
Overview
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