ls -d1 */shrink* | perl -ne 'chomp; chop; /^(.*?)\_(.*?)\_(.*?)\/shrink\_(.*?)$/ || die "Weird directory name : $_\n"; my $q0=$1; my $s0=$2; my $z=$3; my $fac=$4; my $q = substr($q0,0,4); my $s = substr($s0,0,4); my $dir=$_;  my $qpdb="$dir\/$q\_.pdb"; my $spdb="$dir\/$s\_\.$fac\.pdb"; my $aln="$q0\_$s0\_$z\/dali.aln"; `../tools/make_structures4LGA_by_seqali.pl $qpdb $spdb $aln`; ' &