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'\" t
.\" Title: DOMAINSSE
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
.\" Date: 08/11/2010
.\" Manual: EMBOSS Manual for Debian
.\" Source: DOMAINATRIX 0.1.0+20100721
.\" Language: English
.\"
.TH "DOMAINSSE" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian"
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.ie \n(.g .ds Aq \(aq
.el .ds Aq '
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.nh
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.SH "NAME"
domainsse \- Add secondary structure records to a DCF file\&.
.SH "SYNOPSIS"
.HP \w'\fBdomainsse\fR\ 'u
\fBdomainsse\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dccfdir\ \fR\fB\fIdirectory\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBdomainsse\fR\ 'u
\fBdomainsse\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBdomainsse\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
This option specifies the name of the DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq 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\&.
.RE
.PP
\fB\-dccfdir\fR \fIdirectory\fR
.RS 4
This option specifies the location of the domain CCF file (clean coordinate files) (input)\&. A \*(Aqclean cordinate file\*(Aq contains protein coordinate and derived data for a single PDB file (\*(Aqprotein clean coordinate file\*(Aq) or a single domain from SCOP or CATH (\*(Aqdomain clean coordinate file\*(Aq), in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \*(Aqcleaned\-up\*(Aq 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: \&./
.RE
.SS "Required section"
.SS "Advanced section"
.SS "Output section"
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
This option specifies the name of the DCF file (domain classification file) with secondary structure records (output)\&. A \*(Aqdomain classification file\*(Aq 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\&.
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
This option specifies the name of the DOMAINSSE log file\&. Default value: domainsse\&.log
.RE
.SH "BUGS"
.PP
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)\&.
.SH "SEE ALSO"
.PP
domainsse is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
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\&.
.sp
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