3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Miguel on October 05, 2006, 09:32:08 am

Title: h-twist vs. twist
Post by: Miguel 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
Title:
Post by: xiangjun 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. (http://http://rutchem.rutgers.edu/~xiangjun/3DNA/albany/luJun092003.txt)

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