SPratt2 documentation

Installation

You also need the dssp program dsspcmbi that can be obtained separately.

Running SPratt2

spratt2 <filename> <maxdist> <minangle> <min_support> <max_rmsd>
    where filename is the name of a file containing PDB file names
          maxdist is in angstrom max dist between
                  two neighbours
          minangle is the minimum cosine value
          min_support is the minimum number of structures to match a pattern
          max_rmsd is the maximum rms deviation between a pattern and a match

List of structures:

SPratt2 takes as input a file containing a list of filenames/PDB identities. It is assumed that the structures to be analysed are present in the working directory each with a filename identical to its PDB id. PDB ids are by convention four characters long. If only one chain from a PDB entry is to be read, the identity of the chain should be given as a fifth letter, e.g., 1flmA identifies the file 1flm, chain A.
An example of an input file to SPratt2:
1hud
1gcb
1fieA
1aim
1ppn SPratt2 also reads a dssp output file for each structure. In the example, SPratt2 will look for 1hud.dssp, 1gcb.dssp, 1fie.dssp, 1iam.dssp, 1ppn.dssp. This can be produced by dsspcmbi that must be obtained separately and run prior to SPratt2. In order to avoid the time consuming parsing of PDB and dssp files each time the program is run, SPratt2 will produce binary files containing the necassary information about each structure. In the example, the first time SPratt2 is run, it will read the pdb and dssp files and produce binary files 1hud.bin, 1gcb.bin, 1fieA.bin, ... The next time the same structures are analysed, the binary files will be read.

maxdist

This is the maximum distance (in angstroms) between two residues for them to be considered as neighbours. Typical values are 8, 10, 12.

minangle

To reduce the lengths of neighbour strings and still keep the residues most likely to be interacting, i.e., residues facing eachother. Residues i and j are facing each other if angle i and angle j both have cosine values larger than or equal to minangle. Angle i is the angle between the vector from c alpha i to c alpha j and the vector from c alpha i to mean side chain atom i. Angle j is the angle between the vector from c alpha j to c alpha i and the vector from c alpha j to mean side chain atom j. If minangle=-1, all residues within maxdist from residue i will be included in residue i's neighbour string. If minangle=0, all residues within distance maxdist that are facing roughly towards i (and i towards them) will be included in residue i's neighbour string.

minsupport

This is the minimum number of structures to match a structure pattern.

max_rmsd

This is the maximum root mean square deviation to be accepted when superposing a possible pattern match onto the pattern.

Running postp

postp <pattern file> <pdbids file> <scop file> [options]
where pattern file is a spratt2 output file
      pdbids file is a file with the IDs of the structures analysed by spratt2
      scop file is a file with scop IDs for the pdbids
subset options:    -nr      - patterns ranked by support 
                   -sc      - patterns ranked by score 
                   -cover   - gives subset of patterns covering structure set
                   -all     - include all patterns
output format:     -html    - produce html output 
                   -latex   - produce latex output (not yet supported)

Example