Thanks for posting that! Although the ProFit invocation there is not isolated from your case-specific code, it's still very useful to see how should the system calls be done. About the wrapper I was thinking about a cleaner, more OO interface. Something like:

my $profitter = Bio::Tools::Run::ProFit->new(
   files     => \@pdbfiles,
   reference => $pdbreference
);

$profitter->fit;
my %rmsds = $profitter->get_rmsds;
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But then, since I haven't used the program much, I don't know what else it could/should do. If I ever need to use it again, I'll get back to this thread and, with your permission, steal the portions of your code that successfully interact with ProFit.