Barcode constraint file

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    • #497
      Anonymous

        Hi,
        I am trying to define a barcode constraint file for a full atom refinement of a comparative model. Could the format for the SSPAIR be further explained?

        SSPAIR

        Does the weight go from 0.0 to 1.0? What cards/characters do I use to define parallel vs. antiparalled B-strands? It would be a perfect example if the following description was put in the proper format: an antiparallel B-strand between residues 4-8 in strand A and residues 16-20 in strand B. Also, can the same residues be used in two instances (to define a sheet)? Thank you very much.

        Reza

      • #4089
        Anonymous

          > Hi,
          > I am trying to define a barcode constraint file for a full atom refinement of a comparative model. Could the format for the SSPAIR be further explained?
          >
          > SSPAIR
          >
          > Does the weight go from 0.0 to 1.0? What cards/characters do I use to define parallel vs. antiparalled B-strands? It would be a perfect example if the following description was put in the proper format: an antiparallel B-strand between residues 4-8 in strand A and residues 16-20 in strand B. Also, can the same residues be used in two instances (to define a sheet)? Thank you very much.
          >
          > Reza
          >

          I think the weight can be any float but negative values give a bonus and positive values give a penalty.

          You use ‘A’ for antiparallel and ‘P’ for parallel orientation.

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