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Miscellaneous items => FAQs => Topic started by: xiangjun on November 29, 2018, 12:45:17 pm

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Title: How to draw a helical axis
Post by: xiangjun 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 (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.

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.