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Author Topic: How to draw a helical axis  (Read 128 times)

Offline xiangjun

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How to draw a helical axis
« on: November 29, 2018, 12:45:17 pm »
While experimentally-determined DNA/RNA double helices (as deposited in the PDB) are never strictly linear, oligonucleotides or fragments of large nucleic acid molecules may be approximately straight. In such cases, it is informative to draw a helical axis to visualize them in a 3D molecular viewer (such as PyMOL or Jmol). Moreover, helical axes from two different fragments can be used to determine the "bending angle" between them. 3DNA and DSSR provide this info, as illustrated below using PDB id 355d as an example.
  • Running 3DNA (v2.3) find_pair 355d.pdb | analyze, the output file 355d.out contains the following segment:
    Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
    Deviation from regular linear helix: 3.30(0.52)
    Helix:    -0.1269   -0.2753   -0.9530
    HETATM 9998  XS    X X 999      17.536  25.713  25.665
    HETATM 9999  XE    X X 999      12.911  15.677  -9.080
    Average and standard deviation of helix radius:
          P: 9.42(0.82), O4': 6.37(0.85),  C1': 5.85(0.86)
    The two HETATM records can be copy-and-pasted into the original PDB file. The line can be easily drawn between them, which is the helical axis.

  • Running DSSR: x3dna-dssr -i=355d.pdb --more, the output contains the following segment:
      helix#1[1] bps=12
          strand-1 5'-CGCGAATTCGCG-3'
           bp-type    ||||||||||||
          strand-2 3'-GCGCTTAAGCGC-5'
          helix-form  BBBBBBBBBBB
        helical-rise:   3.30(0.52)
        helical-radius: 9.42(0.82)
        helical-axis:   -0.127    -0.275    -0.953
           point-one:   17.536    25.713    25.665
           point-two:   12.911    15.677    -9.080
    With the --helical-axis option, as in x3dna-dssr -i=355d.pdb --more --helical-axis, DSSR also generates a file named dssr-helicalAxes.pdb with the following content:
    REMARK-DSSR: helix#1
    ATOM      1  P1   DC A   1      17.536  25.713  25.665  1.00 10.97      H1   P
    REMARK-DSSR: helix#1
    ATOM      2  P2   DG A  12      12.911  15.677  -9.080  1.00 18.40      H1   P
    CONECT    1    2
    CONECT    2    1
    Loading both 355d.pdb and dssr-helicalAxes.pdb into PyMOL, one can get an image as attached.
« Last Edit: November 29, 2018, 12:53:24 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.