If I remember correctly the issue that exists with the make_fragments.pl stemmed from the executable blastpbp only being packaged with a legacy version of blast and not blast+. The NR databases are too large at this point to work with the version of blast that they were previously using.
If you only need to get fragments I would just call fragment picker directly with:
fragment_picker.default… -in:file:fasta … -in:file:vall …path_to_vall…
Is there a reason why you need to use the scripts in fragment tools instead?
I had the pdb_to_vall script working on one of my machines back in the fall and I bet I could get the make_fragments script working next weekend if there is something that you need it for.
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