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Author Topic: Different shear etc. 3 DNA and Curves+  (Read 51 times)

Offline ellify

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Different shear etc. 3 DNA and Curves+
« on: September 11, 2019, 08:58:09 am »
I have the following question. I calculated the shear, buckle etc. for a DNA helix ( PDB 355d.pdb  same as the one in "Building a bridge between Curves+ and 3DNA") with 3DNA and with Curves+. I would have expected to get identical values for the shear, buckle roll etc. with both programs. However, that is not the case. e.g. shear for the first base pair using 3DNA is  0.28 and using Curves+ is 0.13, propeller -17.31 resp. -18.5

Why is there such a difference? Is there a different convention/parameters for the calculation in 3DNA compared to Curves+?

I produced the input for curves using  find_pair -c+ and I'm attaching all relevant files.
« Last Edit: September 11, 2019, 10:36:31 am by ellify »

Offline xiangjun

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Re: Different shear etc. 3 DNA and Curves+
« Reply #1 on: September 11, 2019, 11:04:49 am »
Quote
I have the following question. I calculated the shear, buckle etc. for a DNA dimer ( PDB 355d.pdb  same as the one in "Building a bridge between Curves+ and 3DNA") with 3DNA and with Curves+. I would have expected to get identical values for the shear, buckle roll etc. with both programs. However, that is not the case. e.g. shear for the first base pair using 3DNA is  0.28 and using Curves+ is 0.13, propeller -17.31 resp. -18.5

It is unrealistic to expect 3DNA and Curves+ to give identical values of base-pair parameters for a given structure. Even with the same Curves+ program, setting fit=.t. or not would give slightly different results. By adopting the standard base reference frame, 3DNA and Cuves+ give similar (but not identical) values for intra- or inter-base pair parameters. See the following blogposts:
Please also refer to the Web 3DNA 2.0 paper where further comparisons were made between 3DNA and Curves+.

Quote
Why is there such a difference? Is there a different convention/parameters for the calculation in 3DNA compared to Curves+?

As always, the devil is in the details. The differences between 3DNA and Curves+ come mainly from two aspects: (1) they implement the standard base reference frame differently; (2) they use different algorithms to calculate base-pair and step parameters. Since both programs are open source, you are welcome to dig into the technical details.

HTH,

Xiang-Jun


« Last Edit: September 11, 2019, 11:06:39 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.