domainreso(1e) [debian man page]
DOMAINRESO(1e) EMBOSS Manual for Debian DOMAINRESO(1e) 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 BUGS
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). SEE ALSO
domainreso is fully documented via the tfm(1) system. AUTHOR
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Wrote the script used to autogenerate this manual page. COPYRIGHT
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. DOMAINATRIX 0.1.0+20100721 08/11/2010 DOMAINRESO(1e)
Check Out this Related Man Page
SCOPPARSE(1e) EMBOSS Manual for Debian SCOPPARSE(1e) NAME
scopparse - Generate DCF file from raw SCOP files. SYNOPSIS
scopparse -classfile infile -desinfile infile -nosegments boolean -nomultichain boolean [-nominor boolean] -dcffile outfile scopparse -help DESCRIPTION
scopparse 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 -classfile infile This option specifies the name of raw SCOP classification file dir.cla.scop.txt_X.XX (input). This is the raw SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57. -desinfile infile This option specifies the name of raw SCOP description file dir.des.scop.txt_X.XX (input). This is the raw SCOP description file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57. Required section -nosegments boolean This option specifies whether to omit domains comprising of more than one segment. This is necessary if a continuous residue sequence is required. Default value: N -nomultichain boolean This option specifies whether to omit domains comprising segments from more than one chain. This is necessary if a continuous residue sequence is required. Default value: N Additional section -nominor boolean This option specifies whether to omit domains from minor classes (defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'). This is necessary or appropriate for many analyses. Default value: N Output section -dcffile outfile This option specifies the name of SCOP DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from the SCOP or CATH databases. The file is generated by using DOMAINER and is in DCF format (EMBL-like). Domain sequence information can be added to the file by using DOMAINSEQS. Default value: test.scop BUGS
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). SEE ALSO
scopparse is fully documented via the tfm(1) system. AUTHOR
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Wrote the script used to autogenerate this manual page. COPYRIGHT
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. DOMAINATRIX 0.1.0+20100721 08/11/2010 SCOPPARSE(1e)