Fix missing backbone residues

Member Site Forums Rosetta 3 Rosetta 3 – General Fix missing backbone residues

  • This topic has 2 replies, 2 voices, and was last updated 14 years ago by Anonymous.
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    • #593
      Anonymous

        Hi

        I am using the relax app to refine pdb files from modeller. It happens very often that rosetta is unable to get the correct sequence from the file.

        Out of all the chains I refined 381 had 1 or more missing residues and 328 were fine.

        The following is from a file where the methionine was discarded because it lacked missing backbone atoms. In this case it is on the end of a chain but in some case it also happened mid-chain.

        ATOM 1705 O VAL A 220 16.025 -3.646 35.246 1.00 96.44 O

        ATOM 1706 OXT VAL A 220 14.359 -5.093 34.991 1.00 96.44 O

        TER 1706 VAL 220

        ATOM 1707 __N__ MET B 221 10.166 -27.113 58.998 0.00161.24 N

        ATOM 1708 __CA__ MET B 221 10.523 -25.998 58.104 0.00161.24 C

        ATOM 1709 CB MET B 221 11.454 -25.022 58.839 0.00161.24 C

        ATOM 1710 CG MET B 221 11.518 -23.642 58.184 0.00161.24 C

        ATOM 1711 SD MET B 221 9.990 -22.672 58.362 0.00161.24 S

        ATOM 1712 CE MET B 221 10.132 -22.479 60.162 0.00161.24 C

        ATOM 1713 __C __ MET B 221 11.206 -26.475 56.861 0.00161.24 C

        ATOM 1714 __O __ MET B 221 10.862 -26.069 55.752 0.00161.24 O

        ATOM 1715 N ILE B 222 12.172 -27.398 57.020 1.00138.79 N

        ATOM 1716 CA ILE B 222 12.957 -27.839 55.903 1.00138.79 C

        ATOM 1717 CB ILE B 222 14.017 -28.845 56.260 1.00138.79 C

        The N,CA,C and O are all present. I do not understand the reason for the error. Is there any way to fix the problem ?

        I can email some of the offending files if that would help.

        Thanks.

      • #4441
        Anonymous

          Their occupancy column is zero. Check the PDB file format for better descriptors of the columns (from the PDB, not Rosetta). Basically the “0.00” column tells Rosetta that the atom is not present, so Rosetta ignores it. You can just manually change this to a nonzero value to get it to work.

          The nonstandard ordering of the backbone atoms (N CA C O is normal) is also unusual, but I’m not sure it’s a problem.

        • #4443
          Anonymous

            Thanks

            That solves my problem.

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