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Author Topic: DNA FORM A/B  (Read 220 times)

Offline bciezah1

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DNA FORM A/B
« on: July 21, 2017, 02:10:19 pm »
Dear Dr. Xiang-Jun Lu

I have a question, I could see that in the section Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases.
in the output file there is a classification as A like or B-like. However, sometimes I see that the corresponding section appear empty. I copy my output to show you what I mean:

   8 GG/CC   -1.19    8.24    2.31   -9.23    7.09    4.72     A
   9 GG/CC   -1.30    8.29    1.93   -4.17    7.08    4.72     A
  10 GA/TC   -1.49    8.52    1.37   -2.55    8.53    1.31
  11 AG/CT   -1.31    8.33    2.80   -7.37    7.00    5.29     A
  12 GG/CC   -1.10    8.62    2.47   -3.32    8.96    0.43     A

Can you explain, please, what this mean for the software? I mean...I guess this is either not A or not B, what is this?

Thank you very much in advance,

Basilio.
=)

Offline xiangjun

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Re: DNA FORM A/B
« Reply #1 on: July 21, 2017, 02:48:02 pm »
Hi Basilio,

It means not A-, or B-, or TA-like, based on the criteria used in 3DNA. See the source code ana_fncs.c/print_PP() for details. Bear in mind that DNA has more conformational flexibility than the three types can cover.

HTH,

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

Offline bciezah1

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Re: DNA FORM A/B
« Reply #2 on: July 21, 2017, 02:53:37 pm »
I see, I understand. I will also review the source code.Thank you very much.
=)

 

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.