Filter for fixed-bb design using RosettaScript?

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    • February 29, 2020 at 3:47 am #3359
      Anonymous

        Hello,

        If I want to implement fix-bb design (or a slight variation of it) using RosettaScripts, what filter should I use?

        Can I not use a filter if I’m just interested in generating a library of designs from multiple input structures with different backbone conformations?

        Does it make sense to not use a filter, since (to my understanding) the packer will generally pick rotamers that have less energy than the original residue anyways and output a final score for the designed pose?

      • February 29, 2020 at 4:09 am #15175
        Anonymous

          You can use whatever filters you wish.  Personally, I don’t use filters, as I like to see what Rosetta is coming out with. For fixbb, your variance in sequence space won’t be too high, so I don’t think filters will do much, but if you design during FastRelax or FastDesign – which allow bb movement, filters that help your specific design task can be helpful

          • February 29, 2020 at 4:48 am #15176
            Anonymous

              Thanks for the reply.

          • March 2, 2020 at 9:39 pm #15182
            Anonymous

              i also tend to use filters pretty sparingly to throw away only the most egregiously bad designs (e.g. using a ScoreType filter to throw away designs with very high energies).  More useful are simple metrics, which let you measure properties of the final structure and write them out with the structure, so that you can decide after the fact which structures to keep.  See this page for a list of simple metrics: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/SimpleMetrics/SimpleMetrics .  The particular ones that you use depend on what your design objective is.

            • March 2, 2020 at 9:40 pm #15183
              Anonymous

                (But getting back to the other part of your question, if you just want to do exactly what the fixbb application does, but in RosettaScripts, then you should just use the PackRotamersMover and nothing else.  The two are equivalent.)

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