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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.
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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
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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] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.