Messages

1

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« on: February 06, 2025, 09:23:25 pm »

Hi Xiang-Jun,

Thank you so much! I'll take time to explore on it. By the way, last time you said the 3DNA source code is available, where could I find it?

Best,
Jing

2

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« on: February 06, 2025, 12:45:48 am »

Hi Xiang-Jun,

Thanks for replying! I have attached several pictures here. They are G and G pairs. The first two are with the opening ~180, the third picture is with ~-180, and the last two are with ~90.

Best,
Jing

3

General discussions (Q&As) / Opening values and the definition for base-pair parameters

« on: February 03, 2025, 04:44:26 pm »

Hi,

I'm using X3DNA to analyze the base-pair parameters and the base step parameters recently. My structure is parallel-stranded DNA and all the base pairs are non-canonical pairs. I found that some parameters are very different from a standard DNA structure. For example, the opening will have values like 170, -170, 90. I read some of the related posts and papers but still confused about the definitions. So what do the 170s and 90s value mean? And what is the difference between 170 and -170? How does X3DNA calculate the opening, that is, which angle does it actually calculate?

And I also have a further question that how does X3DNA calculate other base-pair parameters? I think I'm getting confused even from the beginning, how were the (o1, x1, y1 ,z1) and (o2, x2, y2, z2) for each base in a certain base-pair defined?

Thanks in advance,
Jing