The binary for SSAP is called
cath-ssap. For usage, run
cath-ssap --help or see below.
Preparing to run SSAP
cath-ssap needs to know where to find PDB files. You can tell it using the
--pdb-path option, which allows you to specify multiple directories in the order they should be searched by separating them with colons (
cath-ssap --pdb-path .:/global_pdbs 1cukA01 1bvsA01
Similarly, you can specify the style of prefix/suffix you use for your PDB files, with the
Since these options' values will typically be fairly stable, it can be tedious to specify them every time. Fortunately, the cath-tools allow their all their command-line options to also be specified via environment variables, eg:
export CATH_TOOLS_PDB_PATH=.:/global/data/directories/pdb export CATH_TOOLS_PDB_PREFIX=pdb export CATH_TOOLS_PDB_SUFFIX=.ent
The defaults values for these parameters are included in the usage information (run
cath-ssap --help or see below).
Once you've set up these environment variables, you can use a command like:
cath-ssap 1cukA 1bvsA
This prints a short summary of the resulting scores (see
cath-ssap --scores-help for format) and writes an alignment file to the current directory (see
cath-ssap --alignment-help for format).
Once you've aligned structures with
cath-ssap, you can make better-looking superpositions with
The current usage information is:
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
DSSP, WOLF and sec
cath-ssap is also able to read its input from other combinations of input files:
- PDB and DSSP
- PDB, DSSP and SEC
- WOLF and SEC
To generate DSSP and sec files from PDB files, you can use:
dssp, the CMBI tool for generating DSSP files from PDB files
secmake, a tool for generating sec files from PDB + DSSP files
Once you've prepared these files, you need to tell
cath-ssap where to find them. This can be done in the same way as for PDBs (see above) using the environment variables
CATH_TOOLS_SEC_PATH (and for non-standard prefixes/suffixes
Please tell us about your cath-tools bugs/suggestions here.