Usage
Usage: cath-ssap [options] <protein1> <protein2>
Run a SSAP pairwise structural alignment
[algorithm devised by C A Orengo and W R Taylor, see --citation-help]
cath-ssap uses two types of structural comparison:
1. Fast SSAP: a quick secondary-structure based SSAP alignment
2. Slow SSAP: residue alignment only
If both structures have more than one SS element, a fast SSAP is run first. If the fast SSAP score isn't good, another fast SSAP is run with looser cutoffs. If the (best) fast SSAP score isn't good, a slow SSAP is run. Only the best of these scores is output. These behaviours can be configured using the parameters below.)
Miscellaneous:
-h [ --help ] Output help message
-v [ --version ] Output version information
Standard SSAP options:
--debug Output debugging information
-o [ --outfile ] <file> [DEPRECATED] Output scores to <file> rather than to stdout
--clique-file <file> Read clique from <file>
--domin-file <file> Read domin from <file>
--max-score-to-fast-rerun <score> (=65) Run a second fast SSAP with looser cutoffs if the first fast SSAP's score falls below <score>
--max-score-to-slow-rerun <score> (=75) Perform a slow SSAP if the (best) fast SSAP score falls below <score>
--slow-ssap-only Don't try any fast SSAPs; only use slow SSAP
--local-ssap-score [DEPRECATED] Normalise the SSAP score over the length of the smallest domain rather than the largest
--all-scores [DEPRECATED] Output all SSAP scores from fast and slow runs, not just the highest
--prot-src-files <set> (=PDB) Read the protein data from the set of files <set>, of available sets:
PDB, PDB_DSSP, PDB_DSSP_SEC, WOLF_SEC
--supdir <dir> [DEPRECATED] Output a superposition to directory <dir>
--aligndir <dir> (=".") Write alignment to directory <dir>
--min-score-for-files <score> (=0) Only output alignment/superposition files if the SSAP score exceeds <score>
--min-sup-score <score> (=-0.25) [DEPRECATED] Calculate superposition based on the residue-pairs with scores greater than <score>
--rasmol-script [DEPRECATED] Write a rasmol superposition script to load and colour the superposed structures
--xmlsup [DEPRECATED] Write a small xml superposition file, from which a larger superposition file can be reconstructed
Conversion between a protein's name and its data files:
--pdb-path <path> (=.) Search for PDB files using the path <path>
--dssp-path <path> (=.) Search for DSSP files using the path <path>
--wolf-path <path> (=.) Search for wolf files using the path <path>
--sec-path <path> (=.) Search for sec files using the path <path>
--pdb-prefix <pre> Prepend the prefix <pre> to a protein's name to form its PDB filename
--dssp-prefix <pre> Prepend the prefix <pre> to a protein's name to form its DSSP filename
--wolf-prefix <pre> Prepend the prefix <pre> to a protein's name to form its wolf filename
--sec-prefix <pre> Prepend the prefix <pre> to a protein's name to form its sec filename
--pdb-suffix <suf> Append the suffix <suf> to a protein's name to form its PDB filename
--dssp-suffix <suf> (=.dssp) Append the suffix <suf> to a protein's name to form its DSSP filename
--wolf-suffix <suf> (=.wolf) Append the suffix <suf> to a protein's name to form its wolf filename
--sec-suffix <suf> (=.sec) Append the suffix <suf> to a protein's name to form its sec filename
Regions:
--align-regions <regions> Handle region(s) <regions> as the alignment part of the structure.
May be specified multiple times, in correspondence with the structures.
Format is: D[5inwB02]251-348:B,408-416A:B
(Put <regions> in quotes to prevent the square brackets confusing your shell ("No match"))
Detailed help:
--alignment-help Help on alignment format
--citation-help Help on SSAP authorship & how to cite it
--scores-help Help on scores format
Please tell us your cath-tools bugs/suggestions : https://github.com/UCLOrengoGroup/cath-tools/issues/new
