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Author Topic: h-twist vs. twist  (Read 9336 times)

Offline Miguel

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h-twist vs. twist
« on: October 05, 2006, 09:32:08 am »
h-twist vs. twist

when running X3DNA the files bp_helical.par and bp_step.par are created. The latter contains
the parameter twist, and the former the parameter h-twist. What does h-twist stand for? helical-twist?
What is the difference between h-twist and twist?

We're working on artificial and natural DNAs and would like to plot an MD-average of the twist
parameter for these duplexes. However, we're not sure whether to plot h-twist or twist.

thanks

Offline xiangjun

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« Reply #1 on: October 05, 2006, 10:02:58 pm »
Hi,

As you guessed, h-twist stands for helical twist. More background info can be found in this email before the 2003 Albany conversation.

Basically, shift, slide, rise, tilt, roll and twist describes the bp stacking geometry, and x-displacement, y-displacement, helical rise, inclination, tip, and helical twist describes the helical geometry. For an ideal B-DNA structure, rise and helical rise would be identical, so are twist and helical twist. For A-DNA, where the bps are not perfectly parallel, you will see a clear difference between the two sets (please also refer to Figure 4 in the 3DNA paper).

In 3DNA definition, the two sets of parameters are rigorously convertible, as seen in eqs. 3 and 4 of 3DNA paper. There is a utility program named 'step_hel' which converts between the two sets of parameters for your verification.

In general use, people talk more about slide/roll/twist etc than x-disp, helical rise etc.

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.