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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. Why I put this in I can't remember, but it must have been useful for something.

Geoff Barton