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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 (http://forum.x3dna.org/faqs/how-to-calculate-dna-bending-angle/)" between them. 3DNA and DSSR provide this info, as illustrated below using PDB id 355d (https://www.rcsb.org/structure/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.