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EMBOSS: interface |
This package is still being developed.
Please ignore this program until further details can be documented.
All further queries should go to Jon Ison. (Jon Ison)
% interface
Mandatory qualifiers: [-in] infile Coordinate file for input (embl-like format) [-out] outfile Contact file for output [-thresh] float Threshold contact distance Optional qualifiers: (none) Advanced qualifiers: -ignore float If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. -vdwf string Name of data file with van der Waals radii -conerrf outfile Name of log file for the build General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-in] (Parameter 1) |
Coordinate file for input (embl-like format) | Input file | test.pxyz |
[-out] (Parameter 2) |
Contact file for output | Output file | test.con |
[-thresh] (Parameter 3) |
Threshold contact distance | Any integer value | 6.0 |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-ignore | If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. | Any integer value | 20.0 |
-vdwf | Name of data file with van der Waals radii | Any string is accepted | Evdw.dat |
-conerrf | Name of log file for the build | Output file | interface.log |
Program name | Description |
---|---|
contacts | Reads coordinate files and writes contact files |
dichet | Parse dictionary of heterogen groups |
psiblasts | Runs PSI-BLAST given scopalign alignments |
scopalign | Generate alignments for SCOP families |
seqsort | Removes ambiguities from a set of hits resulting from a database search |
siggen | Generates a sparse protein signature |
sigscan | Scans a sparse protein signature against swissprot |