Help with pyRosetta python scripting for protein manipulation

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    • #1293

        We have recently begun learning to use pyRosetta. We have been using Foldit (both standalone and the online game version) for a while to do some protein modelling. The online version of Foldit has easy to use Lua scripts that make protein manipulation very easy but we can’t export the pdb files. We would like to be able to do similar scripting in pyRosetta that we can do in Lua. Does anyone have information on how the Foldit Lua script commands translate to equivalent functions in pyRosetta? For example, what is the equivalent of foldit’s rubber-bands in pyRosetta? What about “freezing” portions of the structure? We would like to take some of the scripts we have developed in Lua and translate them to pyRosetta. We would love to have the Lua scripting in foldit standalone but that’s not there yet. We have seen the online tutorial for pyRosetta but was wondering if there are more example scripts out there that people are sharing that we have not found yet.

        thanks for any hints, help or suggestions!

      • #7172

          Have you tried posting this on the FoldIt boards? I don’t know who, if anyone, in the FoldIt group monitors those boards, but they’re more likely to know how to translate FoldIt Lua to PyRosetta Python than I am.

        • #7173

            Thanks! We will try that. Do you know of any centralized location where the pyRosetta community shares scripts?

          • #7219

              Rubber bands in Foldit correspond to constraints (specifically AtomPair constraints) in Rosetta/PyRosetta.

              There isn’t any general “freezing” functionality in Rosetta, but the same can be accomplished by use of appropriate settings to PackerTasks (for packing — “shake” in Foldit parlance) and MoveMaps (for minimization — “wiggle” in Foldit).

            • #7174

                Things will occasionally get posted here; other than that there’s the main repository on the pyrosetta page ( I’m not aware of anything other than that. I’m sure Sergey would post submitted scripts.

              • #7250

                  Thanks much, that’s very helpful!

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