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Author Topic: nucleic acid sugar structure  (Read 634 times)

Offline lvelve0901

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nucleic acid sugar structure
« on: February 21, 2017, 01:13:21 pm »
Hi, xiangjun,

Here is the snapshot of a deoxyribose in a idealized B-form generated by 3DNA and some distance and angle measurement.

I am just curious where these bond length and bond angle details come from. How do you build the idealized model? Is it purely from previous crystal structure or literature. Or you build them based on your own criteria.

Best,
Honglue

Offline xiangjun

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Re: nucleic acid sugar structure
« Reply #1 on: February 21, 2017, 01:59:23 pm »
What 3DNA command did you use to generate the idealized B-DNA model? Please be specific by providing a reproducible example.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: nucleic acid sugar structure
« Reply #2 on: February 21, 2017, 06:42:23 pm »
I type:

fiber -b -seq=A ATbp.pdb

Offline xiangjun

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Re: nucleic acid sugar structure
« Reply #3 on: February 21, 2017, 06:49:05 pm »
Read the 3DNA 2003 NAR paper, and type fiber -h (plus fiber -m) to see from where the fiber models in 3DNA are derived. It helps, both to yourself and the community, that you report back your findings.

Xiang-Jun
« Last Edit: February 22, 2017, 01:34:41 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.