I am not sure that this is the right forum to post my question as I am using CS-Rosetta instead of Rosetta, but nevertheless it may be worth a try. I have been trying to generate fragments using the runCSRjob3.com script. It can generate the initial **.mfr.tab files correctly. However, it does not generate the **.rosetta.tab files correctly (they are empty). There may be an issue with the mfr2rosetta.com script but I am not sure what. It keeps telling me that there is an error in the fragment candidates. I am using a solid state CS table, but I believe that should not be an issue. It also generated 200 fragment candidates, so the CS table should be fine. I tried using the mfr2rosetta.com script separately but that gave me the same error message.
Any help would be highly appreciated.