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Re: Rearrange the residue number of a pdb file according to the residues names

by pme (Prior)
on Jun 18, 2015 at 11:36 UTC ( #1130975=note: print w/replies, xml ) Need Help??


in reply to Rearrange the residue number of a pdb file according to the residues names

Hi nastaziales,

Welcome to the monastery! Could you explain what to do with $m3 and $m5?

  • Comment on Re: Rearrange the residue number of a pdb file according to the residues names

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Re^2: Rearrange the residue number of a pdb file according to the residues names
by nastaziales (Initiate) on Jun 18, 2015 at 12:17 UTC
    an example of a pdb file:
    ATOM 1 N LEU A 579 -44.254 33.292 -5.352 1.00 92.25 ATOM 2 CA LEU A 579 -43.296 32.939 -4.304 1.00 88.51 ATOM 3 C LEU A 579 -43.865 33.305 -2.916 1.00 94.93 ATOM 4 O LEU A 579 -44.226 34.459 -2.677 1.00 97.79 ATOM 5 CB LEU A 579 -41.945 33.627 -4.567 1.00 88.70 ATOM 6 CG LEU A 579 -40.668 32.828 -4.289 1.00 88.54 ATOM 7 CD1 LEU A 579 -40.298 31.909 -5.470 1.00 87.89 ATOM 8 CD2 LEU A 579 -39.515 33.759 -4.003 1.00 90.97 ATOM 9 1H LEU A 579 -45.070 33.694 -4.937 1.00 99.99 ATOM 10 2H LEU A 579 -43.920 33.952 -6.025 1.00 99.99 ATOM 11 3H LEU A 579 -44.567 32.526 -5.914 1.00 99.99 ATOM 12 N SER A 580 -43.966 32.299 -2.017 1.00 89.98 ATOM 13 CA SER A 580 -44.572 32.440 -0.687 1.00 90.11 ATOM 14 C SER A 580 -43.866 31.761 0.494 1.00 88.81 ATOM 15 O SER A 580 -43.564 30.563 0.472 1.00 84.43 ATOM 16 CB SER A 580 -46.046 32.049 -0.724 1.00 96.32 ATOM 17 OG SER A 580 -46.293 31.048 -1.698 1.00107.02 ATOM 18 H SER A 580 -43.643 31.364 -2.161 1.00 99.99
    the 4rth column is the residue name and the 6th the residue number, i need a script that will rearrange the residue number according to the residue name (when the previous residue name of the column is the same with the next one then the residue number is the same too, when it changes the residue number should have a +1)
      Can you give an example input and desired output?

      -QM
      --
      Quantum Mechanics: The dreams stuff is made of

      m3 is the residue name and m5 the residue number

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