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;

[download]
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.

In reply to Re^3: open3 buffering in linux vs. os x by bruno
in thread open3 buffering in linux vs. os x by Lexicon

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