cath-ssap

Downloads

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 (:), eg:

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 --pdb-prefix and --pdb-suffix options.

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).

Running SSAP

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 cath-superpose.

Usage

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

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_DSSP_PATH and CATH_TOOLS_SEC_PATH (and for non-standard prefixes/suffixes CATH_TOOLS_DSSP_PREFIX, CATH_TOOLS_SEC_PREFIX, CATH_TOOLS_DSSP_SUFFIX and CATH_TOOLS_SEC_SUFFIX).

Feedback

Please tell us about your cath-tools bugs/suggestions here.