double mutations scan

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    • April 27, 2012 at 7:51 pm #1257
      Anonymous

        Dear ALL,
        I try to scan all the possible double mutations use this command”~/rosettabin/pmut_scan_parallel.macosgccrelease -database ~/rosettadb -s 1ABC.pdb.gz -double_mutant_scan -output_mutant_structures -ex1 -ex2 -extrachi_cutoff 1 -use_input_sc
        -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core”.
        But I also want to fix all the residues as NATRO except the mutated residues. What command should I use? Thank you!

      • April 28, 2012 at 3:00 am #7033
        anumglasgow
        Participant

          Lindsay,
          At this time, the pmut_scan_parallel app can’t take a resfile (which would allow you to give residue-specific behaviors like NATRO). That’s an interesting idea, though. Perhaps I can add that in and have it as part of the next release.
          Since you have an idea of which residues should be allowed to mutate and which to hold fixed, you can put that into a resfile, run a few dozen fixbb trajectories and then generate a sequence profile of the results. You can usually tell from that which positions Rosetta thinks are important for increasing stability.

        • April 30, 2012 at 2:01 pm #7049
          Anonymous

            Dear ronj,
            If I read guild line from the resfile, I have to load the rosetta database many times. Is there any way to load it once and reuse it again and again? Or is there any way to tell the rosetta to design only two residues I give but not other residues (NATRO). Thank you.

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