3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: bciezah1 on April 04, 2017, 11:02:42 pm

Title: Minor and major grove calculation
Post by: bciezah1 on April 04, 2017, 11:02:42 pm: Dear Xiang-Jun,

I would like to understand why I got this output when I calculated the minor and major groove from my pdb. It seems that there is some miss values. I attached the pdb I used (I am using 3DNA v2.0)

Thanks you in advance,

Basilio.

Minor Groove Major Groove
P-P Refined P-P Refined
1 AA/TT --- --- --- ---
2 AA/TT --- --- --- ---
3 AA/TT 9.2 --- 20.8 ---
4 AA/TT 9.2 9.1 21.1 21.1
5 AA/TT 9.6 --- 20.1 ---
6 AA/TT --- --- --- ---
7 AA/TT --- --- --- ---
8 AA/TT --- --- --- ---
9 AA/TT --- --- --- ---
10 AA/TT --- --- --- ---
11 AA/TT 10.9 --- 19.3 ---
12 AA/TT 10.6 10.3 18.7 18.4
13 AA/TT 9.9 9.7 19.5 19.2
14 AA/TT 10.4 10.3 20.7 20.7
15 AA/TT 10.6 --- 18.7 ---
16 AA/TT --- --- --- ---
17 AA/TT --- --- --- ---
Title: Re: Minor and major grove calculation
Post by: xiangjun on April 04, 2017, 11:10:25 pm: Please upgrade 3DNA v2.3, that's the latest version. See $X3DNA/doc/groove-widths.pdf for the original El Hassan & Calladine reference.

Xiang-Jun