why w3DNA fails to calculate some non-canonical base pairs in structure

[Ying]

Dear Xiang-Jun,

I used the 3DNA web sever before, but there are several base pairs missing during the calculation, which may result in the incorrect calculation for the width of the major and minor groove of our RNA structure. I searched the forum and found that it may be due to the default setting for the website. Could you give me some suggestions on this problem?  Thank you very much for your help.

Best wishes,

Ying

[xiangjun]

Please provide a concrete example.

[Ying]

Dear Xiang-Jun,

Attached please find the part of analysis done via w3DNA for my PDB, and I found that the analysis just escape 4 adenosines for all types of calculation. The sequence (5'---3') is GGGC(CAG)5GUCC. Thank you very much for your help.

Best wishes,

Ying

[xiangjun]

Hi Ying,

Given the information you provided, I can only conclude that there must be some oddity in your structure at the places where 3DNA is unable to detect the base pairs. I cannot provide any further advice before seeing the structure (or the relevant section of it).

Xiang-Jun