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Questions and answers => General discussions (Q&As) => Topic started by: lvelve0901 on February 09, 2017, 05:39:06 pm

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Title: Swap the dinucleotide step index
Post by: lvelve0901 on February 09, 2017, 05:39:06 pm

Hi, xiangjun,

I have a general question about the coordinate frame.

For a given dinucleotide step, you can swap the dinucleotide step (5'-CA-3' ==> (3'-AC-5') 5'-TG-3') by renumber the residue id and the sign of shear, buckle, shift, tilt, y-displacement and tip will also be swapped.

Could you kindly explain to me? Is it because the coordinate frame changes? Does that mean we should be cautious to interpret the sign of those parameters above when we analyze structure?

Best,
Honglue

Title: Re: Swap the dinucleotide step index
Post by: xiangjun on February 09, 2017, 06:03:42 pm

Hi,

The parameters are a measure of relative position and orientation of one unit to the other. It is natural that when you swap the two strands of a dinucleotide step, or the two bases in a pair, some parameters have their signs reversed. You can easiy see such cases in real lifes.

The technical details PDF distributed with 3DNA v2.3 contains concrete examples for users to follow. To see how swapping the two strands would effect the parameters, you are welcome to repeat the process. It helps if you could share your experience here.

Also note that 3DNA v2.3 is open source. You're encouraged to dig into the details as you see fit.

Best regards,

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.