foreach my $ref (keys %$self){
   next unless $self->{$ref}{'chain'} = 1;
   # process chain 1 atoms 
}

##</code><code>##

foreach my $ref (keys %$data){
   next unless $data->{$ref}->type eq 'ATOM';
   my $atom = $data->{$ref}->atom;
   $self->{$atom->chainId}{$ref}{atoms} = $atom;
   $self->{$atom->chainId}{$ref}{'residues'} = $atom->resNumber;
}
# ...
foreach my $ref (keys %{$self->{1}}) {
   # process chain 1 atoms
}