This is the command scopparsee 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
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
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