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I’m told you got an answer straight from Nikolaos Sgourakis, but to archive it for the sake of other users:
“the new fragment picker application will be included in the new Rosetta 3.3 which is going to be released soon. We have already replied to Marcel internally.
His best bet right now is to use the mfr picker developed by Yang Shen at the NIH, and works ok for getting fragments.