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    Thank you very much for the prompt response. A quick followup:

    Am I correct in my approach to getting coordinates of the lowest energy structure by having the program write all the pdb files (using -out:file:fullatom flag)? I then look at the score file and find which of the written structures has the lowest energy.

    Or is there a way to not write each pdb structure and instead only write pdb files for the structures you are interested in afterwards?