3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: sjo248 on March 18, 2015, 10:53:59 am

Title: What is the difference between direct P-P measurement and refined
Post by: sjo248 on March 18, 2015, 10:53:59 am: I have searched and cannot find what the difference between the direct P-P measurement and the refined measurement when it comes to major/minor groove widths. Can somebody please help?
Title: Re: What is the difference between direct P-P measurement and refined
Post by: xiangjun on March 18, 2015, 11:45:17 am: Here is an example output for the Dickerson dodecamer (355d), which contains the reference for groove widths 3DNA uses. Specifically, read the two-page appendix of the 1998 El Hassan and Calladine paper.

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**************************************************************************** Minor and major groove widths: direct P-P distances and refined P-P distances which take into account the directions of the sugar-phosphate backbones (Subtract 5.8 Angstrom from the values to take account of the vdw radii of the phosphate groups, and for comparison with FreeHelix and Curves.) Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343. Minor Groove Major Groove P-P Refined P-P Refined 1 CG/CG --- --- --- --- 2 GC/GC --- --- --- --- 3 CG/CG 14.3 --- 18.2 --- 4 GA/TC 12.0 11.9 17.3 17.3 5 AA/TT 9.7 9.6 19.1 19.0 6 AT/AT 9.1 9.1 16.4 16.0 7 TT/AA 9.1 9.1 17.8 17.7 8 TC/GA 9.6 9.6 18.6 18.6 9 CG/CG 10.4 --- 19.0 --- 10 GC/GC --- --- --- --- 11 CG/CG --- --- --- ---
HTH,

Xiang-Jun
Title: Re: What is the difference between direct P-P measurement and refined
Post by: sjo248 on March 18, 2015, 03:24:07 pm: I appreciate your response but I've already read that paper, and again reviewing the appendix didn't give me the answer. I'm a grad student and new to this field, just doing a side project with a different P.I., but he didn't know the difference either. I don't need calculations or anything, I just need to know how the two values differ. I figured someone here would know since its reported in the 3DNA output. Searching this website, or google didn't help me either.
Title: Re: What is the difference between direct P-P measurement and refined
Post by: xiangjun on March 18, 2015, 03:50:24 pm: The reference gives the definition of the two sets of groove widths. I implemented the algorithm reported in the paper after reading through the appendix many times.

Reading the original literature and examining sample 3DNA outputs should allow for a high-level understanding of two sets of groove widths. To really get to the bottom of the issue, I know of no better alternate than to implement the algorithm, which requires calculations and programming. I may misunderstand your question. Others on the Forum may be able to provide a more helpful answer.

You may want to try Curves+ which has a different way of calculating groove widths and depths.

Xiang-Jun