### Author Topic: base pair frame from base frames  (Read 4362 times)

#### jyesselm

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##### base pair frame from base frames
« on: February 26, 2014, 06:40:53 pm »
Hi Xiang-Jun,

I was hoping you could help me understand part of your tech_details.pdf. I was able to follow up to calculating the reference frame of each base and I am trying to understand how you combine them into "middle frame", presumably this is base pair frame? Shown on page 6 for base pair A_G1-B_C8.

Thank you very much.
-Joe

#### xiangjun

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##### Re: base pair frame from base frames
« Reply #1 on: February 26, 2014, 11:19:30 pm »
Hi Joe,

Thanks for reading the doc 'tech_details.pdf' and posting your question on the forum. You're right in noting that the "middle frame" is the base-pair frame used to calculate step parameters (slide, roll, etc). Regarding the details on calculating the "middle frame" for pair A_G1-B_C8, please see the thread "Middle reference frame computation", and also "Question on base-step parameters calculation in 3DNA".

As noted in the Section on "Base-pair parameters" in tech_details.pdf:
Quote
Given the above base reference frames for A_G1,B_C8 and A_G2,B_C7, we can calculate the base-pair parameters (Shear, Stretch, Stagger, Buckle, Propeller, and Opening). The procedure is exactly the same as for step parameters detailed below. Here we just give the parameters for the two base-pairs, and users who are interested in knowing the details should work them through and should get exactly the same numbers.

So once you walk through the Section on "Step parameters", you should be able to get what you want by following the same procedure. You're welcome to post back any issues you may encounter in this adventure.

HTH,

Xiang-Jun

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.