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RNA structures (DSSR) / Re: plotting the helical axis along curved helices
« Last post by xiangjun on October 25, 2024, 08:46:14 pm »Hi Di,
The info is within DSSR, but not exposed. I'm considering to add this feature in DSSR JSON output for easy parsing. For WC-like pairs, things are not that complicated. However, with there are subtitles with non-Watson-Crick pairs, e.g., Hoogsteen and reverse Hoogsteen base pairs.
See "Worked examples on base-pair parameters" in the DSSR Pro User Manual. especially Session "6 Local helical parameters". The vectors o1_h and o2_h are what you need. They are not simple shifts of the origin in the reference frame.
This thread actually prompt me to refine the detailed algorithmic descritpion and get the content published. They are the real meat of 3DNA!
Best regards,
Xiang-Jun
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Do you have any idea of how to easily find the axis of each 2-bp segment of a helix?
The info is within DSSR, but not exposed. I'm considering to add this feature in DSSR JSON output for easy parsing. For WC-like pairs, things are not that complicated. However, with there are subtitles with non-Watson-Crick pairs, e.g., Hoogsteen and reverse Hoogsteen base pairs.
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Also, I think an easier solution for A-form helix is to do a shift of the origin in the plane of the reference frame so that the shifted origin is where the axis passes through the plane.
See "Worked examples on base-pair parameters" in the DSSR Pro User Manual. especially Session "6 Local helical parameters". The vectors o1_h and o2_h are what you need. They are not simple shifts of the origin in the reference frame.
This thread actually prompt me to refine the detailed algorithmic descritpion and get the content published. They are the real meat of 3DNA!
Best regards,
Xiang-Jun