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    I’ve never tried RMSD with FloppyTail. FloppyTail does not directly support it (it does not take in:file:native as you tried).

    You tried the right thing: using the score app to get RMSDs. Try it with the Rosetta 3.1, since the score_jd2 in Rosetta3.2 won’t work. Once you have those RMSDs you should be set. (You can install 3.1 and 3.2 on one computer; they won’t “know about” each other and won’t conflict. You may need two copies of the database. I have about 10 Rosetta installations on my computer…)