sequence variability in rosetta design

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    • October 15, 2009 at 10:44 am #356
      RituparnaSamanta
      Participant

        Hello,
        Is there any way to increase sequence variability during design?
        For some positions I get all the time one type of residue (charged on the surface) and I would prefer to see other options even by the cost of energy.

        command I use:

        -design -fixbb -sym_des_units 2 -profile -ndruns 10000 -read_all_chains -fa_output -extra_chi_cutoff 1 -ex1 -ex2aro_only -soft_rep_design

        Thank you in advance for hints
        Staszek

      • October 19, 2009 at 1:58 pm #4235
        Anonymous

          There isn’t really a good way to make the packer perform non-optimally. If it’s just one position, I’d suggest making a resfile which forbids the residues you don’t want at that one position:

          …
          # # PIKAA AFGILMNPQSTVWY
          …

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