Symmetric Processing for evaluating side-chain of chi angle

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    • #1429

        I have some problems about evaluating side-chain of chi angle. I used executable file of “relax” to repack side-chain, then I want to evaluate the number of chi angles which are lower than 40 degrees comparing with native angle. I associate something, as follows:
        1、amino acids ,like ASP , GLU, PHE, TYR, ARG, etc ,having symmetry, are evaluated with symmetrical processing, in order to avoid error calculation coursed by the numbers of the same atomic.
        2、For ASN, GLU, HIS this kind of amino acids, C and N in crystallography can’t distinguish. in this case we also should make symmetrical processing.
        As mentioned above,how can I Make use of rosetta to solve this problem. I think rosetta should pay attention to this. because I haven’t familiar with the code of rosetta, I still did not find it at present. I hope you can give me some help, Thank you!

      • #7898

          I am so sorry that I might inching the button of saving twice, but I can’t find deleting button in the editting page.

        • #7899

            Don’t worry about double-posting, I took care of it. (You didn’t fail to find the button – it’s simply not there for non-administrator users).

            The term Rosetta uses to calculate what you want is “rotamer recovery”. There is a way to do two-structure-comparison rotamer recovery in the way that you want…but unfortunately it was written after Rosetta3.4 was released, and so it hasn’t been released yet. There are several tools in Rosetta3.4 that test rotamer recovery by making changes and then immediately checking rotamer recovery, but none that will let you feed in two structures at a time (the original, and the modified comparison) and check their similarity to each other.

            Do you want to do this check just to see how much Rosetta changed things, or for a benchmark against some other program, or just to check that Rosetta does things that make sense? The existing rotamer recovery stuff in 3.4 (rosetta_tests/integration/tests/rotamer_recovery) may be enough for your needs in the last case.

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