SORTTRANS

This program takes the output from a scan, and cleans and sorts the output. It removes repeated transformations by a simple least squares comparison of the matrices and vectors for those transformations which have the same identifier.

The format is:

    sorttrans -f <scan output file> -s <keyword> <cutoff> [-t -i]

-f reads output from STAMP scanning, -s tells the program how to sort the output. The keyword tells which method to use. There are 8 possible keywords:

    Sc              sort by Sc
    rms             RMS deviaition
    nfit            number of fitted atoms
    len             alignment length
    frac            nfit/len
    q_frac          nfit/q_len (q_len = length of query structure)
    d_frac          nfit/d_len (d_len = length of database structure)
    n_sec           number of equivalent secondary structure elements
    seq_id          percent  sequence identity
    sec_id          percent secondary structure identity

sorted transformations are written to the standard output.
The option -i ==$>$ identifiers only. Consider only the best transformation per identifier.

The option -n ==$>$ ignore domain descriptors. This means that only the filename and the transformations are used. This is useful if you have different domain names attributed to the same region of the structure.