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Author Topic: BI and BII conformations  (Read 10428 times)

Offline caterina.bianchi

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BI and BII conformations
« on: April 10, 2013, 12:04:05 pm »
Dear Xiang,

I was reading on the 3DNA hompage that we defined the ranges for BI and BII conformations, but I don't understand what is the range for e-z. Is it -180 to +180 or -360 to +360?

Thanks in advance.

Best regards,

Caterina Bianchi

Offline xiangjun

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Re: BI and BII conformations
« Reply #1 on: April 10, 2013, 05:16:41 pm »
It is a good question; the short answer is that the range of e-z is in [0, 360].

In 3DNA, the backbone BI/BII classification is based on e-z and works as below:
  • It follows the definition as given by IMB Jena, "Nucleic acid backbone parameters". Specifically,
    BI:  (epsilon-zeta) = -160° ... +20°
    BII: (epsilon-zeta) = +20° ... +200°
  • In 3DNA, all torsion angles are given in the range of [-180, +180]. To calculate e-z, epsilon and zeta are first converted to [0, 360]. If the difference (d=e-z) is < 0, then d=d+360. So d should be in [0, 360]. If d is in [20, 200], it is classified as BII, otherwise, BI.
Does that make sense? If you know of any more elaborate definition of the BI/BII conformations, please let me know.

Xiang-Jun
« Last Edit: April 10, 2013, 06:11:29 pm by xiangjun »

Offline caterina.bianchi

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Re: BI and BII conformations
« Reply #2 on: April 11, 2013, 05:18:06 am »
Dear Xiang,

Thanks for your reply! I have another question, because I don't understand what mean  when you say "If the difference (d=e-z) is < 0, then d=d+360",but in this way the values that I will get will be always positive. How you can get -160 degrees?

Regards,

Caterina Bianchi

Offline xiangjun

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Re: BI and BII conformations
« Reply #3 on: April 11, 2013, 08:54:36 am »
Thanks for your followup. After checking the source code carefully and a sample 3DNA output, I noticed that my previous reply is incomplete (inaccurate)  :(. Thus the discrepancy: you found that e-z can be negative in analyze -tor output, while I said that it's in range [0, 360] which should always be positive.

The missing piece is that the 3DNA reported difference (d=e-z) is the raw value, which can be positive or negative. Only for classifying a BI/BII conformation, negative d value is added 360 to make it positive; this simplify the code since the continuous range 20, 200 is checked for BII conformation.

Does this solve your puzzle? If still not, please post some concrete examples so we can walk them through to get to the bottom of the issue.

Xiang-Jun

Offline caterina.bianchi

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Re: BI and BII conformations
« Reply #4 on: April 12, 2013, 11:21:35 am »
I'm sorry Xiang, but I really didn't understand your reply...
if epsilon = 0 to +360 and zeta= 0 to +360 e-z = -360     0        +360, but how can get negative values in this way?

thanks

Caterina Bianchi

Offline xiangjun

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Re: BI and BII conformations
« Reply #5 on: April 12, 2013, 11:44:05 am »
Quote
if epsilon = 0 to +360 and zeta= 0 to +360 e-z = -360     0        +360, but how can get negative values in this way?

Well, I am a bit confused by your reply too. If epsilon=60, zeta=160, then e-z=60-160=-100, which is NEGATIVE, right?

That's why I asked you to provide some concrete examples to walk through. Okay, let's use PDB  id 355d as an example, if you run the command:
Code: [Select]
analyze -tor=355d.tor 355d.pdb, you will have the following in file 355d.tor:

Code: [Select]
              base      chi A/S     alpha    beta   gamma   delta  epsilon   zeta     e-z BI/BII
------------------------------------------------------------------------------------------------
  10 A:..10_:[.DG]G   -83.6 anti    -60.3   163.2    39.5   143.2  -100.0   146.3   113.6  BII
  11 A:..11_:[.DC]C  -112.8 anti    -73.1   144.3    50.8   143.5  -164.4  -126.1   -38.3  BI

For nt C11, epsilon=-164.4, corresponding to -164.4+360=195.6; whilst zeta=-126.1, corresponding to -126.1+360=233.9; 195.6-233.9=-38.3 which is the value reported in 3DNA (see above). Since -38.3 < 0, 360 is added to it: -38.3+360=321.7, which is out of [20, 200], so it is assigned BI. Please work out the numbers for G10, and report back here.

Does this clarify your confusion?

Xiang-Jun
« Last Edit: April 12, 2013, 12:00:31 pm by xiangjun »

Offline caterina.bianchi

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Re: BI and BII conformations
« Reply #6 on: April 12, 2013, 12:24:20 pm »
epsilon= -100 zeta= 146.3 epsilon = -100+360= 260 epsilon-zeta=260-146.3 = 113.7

Now I understood.

Thanks!


Offline caterina.bianchi

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Re: BI and BII conformations
« Reply #7 on: April 12, 2013, 12:27:22 pm »
ps it's BII conformation because is in the range 20, 200  :D

Offline xiangjun

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Re: BI and BII conformations
« Reply #8 on: April 12, 2013, 12:34:45 pm »
I am glad to see the happy :D. This thread help to illustrate clearly that a concrete example is the most effective and unambiguous way to get a (technical) point across. So in the future, whenever you have a 3DNA-related question, please be specific, and do not hesitate to post on the forum.

Xiang-Jun
« Last Edit: April 12, 2013, 12:36:39 pm by xiangjun »

 

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.