The binary for SSAP is called
cath-ssap. For usage, run
cath-ssap --help or see below.
Preparing to run SSAP
For each protein structure,
cath-ssap requires a PDB file, a DSSP (or wolf) file and a sec file. To generate these 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 your PDB, DSSP/wolf and sec files, you need to tell
cath-ssap where to find them. We recommend you use the path options to manage your list of directories to search. This can be done by specifying command-line options every time you run
cath-ssap, but it may be easier to permanently add suitable environment variables to your profile. For example to tell the the cath-tools to search for the files in the current directory (aka
.) and then your global directories, add environment variables to your profile as follows:
CATH_TOOLS_PDB_PATH .:/global/data/directories/pdb CATH_TOOLS_DSSP_PATH .:/global/data/directories/dssp CATH_TOOLS_SEC_PATH .:/global/data/directories/sec
Similarly, if you use a different style of prefix/suffix for your files, you can specify these with command line options or with these environment variables:
CATH_TOOLS_PDB_PREFIX CATH_TOOLS_DSSP_PREFIX CATH_TOOLS_SEC_PREFIX CATH_TOOLS_PDB_SUFFIX CATH_TOOLS_DSSP_SUFFIX CATH_TOOLS_SEC_SUFFIX
The defaults values for all 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_DSSP_SEC) Read the protein data from the set of files <set>, of available sets: 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 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
Please tell us about your cath-tools bugs/suggestions here.