dssp

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    • October 5, 2017 at 4:34 pm #2749
      Anonymous

        Hello. I have a  questions about abinitio structure prediction.

        How  to chang the DSSP code and let  β-bridge become L , when get a pose secondary structure. I try to change it, but I do not know how to write the code in the  dssp_state method of  StrandPairing.cc in core/scoreing/dssp directory.

        Please teach me method,  if you know , thank you very much!

      • October 10, 2017 at 4:54 pm #13803
        Anonymous

          The Rosetta DSSP code should identify beta bridges as ‘B’ (versus regular beta sheets, which are ‘E’).  Is there some reason that post-processing the results doesn’t work for you? (That is, pull out the DSSP assignments as a string and then use string replacement to replace all the ‘B’s with ‘L’s)

          If you did want to change the assignments by hacking the code, you would just need to find the places where the ‘B’s were assigned. This actually doesn’t happen in src/core/scoring/dssp/Dssp.cc itself, but rather in src/core/scoring/dssp/StrandPairing.cc. At around line  630 or so, you’ll notice a line which is `state = ‘B’;`. If you want Rosetta to classify beta-bridges as ‘L’, just change that line to`state = ‘L’;`.

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