3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: lvelve0901 on February 21, 2017, 01:13:21 pm

Title: nucleic acid sugar structure
Post by: lvelve0901 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
Title: Re: nucleic acid sugar structure
Post by: xiangjun 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
Title: Re: nucleic acid sugar structure
Post by: lvelve0901 on February 21, 2017, 06:42:23 pm: I type:

fiber -b -seq=A ATbp.pdb
Title: Re: nucleic acid sugar structure
Post by: xiangjun 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