ls -d1 */ | perl -ne 'chomp; chop; chop; my $dir=$_; my ($pdb1, $pdb2, $z) = split /\_/, $_; print "$pdb1  $pdb2 $z...\n"; $pdb1_=substr($pdb1,0,4); $pdb2_=substr($pdb2,0,4); system("cd $_; mkdir dali1; cd dali1; DaliLite -pairwise ..\/$pdb1_\.pdb ../$pdb2_\.pdb >& log.tmp"); ' &