I think that you were looking for something like WWW::PDB. This seems easier: 
#!/usr/bin/perl

use strict;
use warnings;
use WWW::PDB qw(:all);

WWW::PDB->cache('/user/Desktop/mech');

my $fh = get_structure('2cu3');
print while <$fh>;

[download]

In reply to Re: using WWW::Mechanize to download a link, opened fine in TextWrangler but as junk in TextEdit by Khen1950fx
in thread using WWW::Mechanize to download a link, opened fine in TextWrangler but as junk in TextEdit by nurulnad

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