usage:
pdbsel5 toyear=2010 method=[X|N|A] gopen=12 gelong=1 nsigma=3 showali=0 matrix=blosum65 chainfile=PDBFIND.TXT selectfile=subset-of-pdb-ids perc=25 minlen=20 maxlen=1000 minrfac=0.0 maxrfac=0.3 minresol=0.0 maxresol=3 minhelix=0 maxhelix=1000 minbeta=0 maxbeta=1000 maxnchains=200000 outfile=pdb-selection-25.12.1

chainfile:  use full PDBFIND.TXT to be downloaded from http://www.cmbi.kun.nl/gv/pdbfinder
gelong:     gap elongation penalty (usually between 1 and 6, default 1)
gopen:      gap open penalty (usually between 8 and 16, default 12)
matrix:     file with distance matrix (default 'blosum.65')
maxbeta:    skip entries with number of beta residues above value (default 10000)
maxhelix:   skip entries with number of helical residues above value (default 10000)
maxlen:     skip chains with more than maxlen amino acid residues (default=100000)
maxnchains: restrict run to input lists with less than maxnchains chains (default 200000)
maxresol:   skip entries with Resolution above value (usually between 0.5 and 5.0, default 3.0)
maxrfac:    skip entries with R-factor above value (usually between 0.1 and 0.4, default 0.3)
method:     use X-rax only (X), NMR only (N), all (A) (default A)
minbeta:    skip entries with number of beta residues below value (default 0)
minhelix:   skip entries with number of helical residues below value (default 0)
minlen:     skip chains with less than minlen amino acid residues (default=25)
minresol:   skip entries with Resolution below value (default 0.0)
minrfac:    skip entries with R-factor below value (default 0.0)
nsigma:     number of SD's used in distance function (usually between 2 and 4, default 3)
outfile:    file with PDBselect list
perc:       homology threshold (between 25 and 95)
selectfile: file with list of PDB-entries to be used as subset from 'chainfile' (thanks to Sergei Rahmanov, Moscow for suggesting this option)
toyear:     skip PDB entries younger than year (default 2999)


A typical call would be:
pdbsel5 matrix=blosum65 chainfile=PDBFIND.TXT perc=25 outfile=max-mueller.pdbselect &