calculating DNA superhelix pitch and radius using 3DNA?

[arvind]

Dear all,
is it possible to calculate the pitch and radius of a DNA superhelix using 3DNA? If yes, how to go about it?

Thanks and Regards,
Arvind

ps: Also it would be a good idea if this user forum is listed on the 3DNA homepage itself. I did not find it there.

[xiangjun]

Dear Arvind,

Thanks for your question regarding calculating the pitch and radius of a DNA superhelix using 3DNA. Unfortunately, it is not possible to perform such calculations in the current version. I do, however, have a interest in adding such functionality in future release of 3DNA. To this end, we need users' collaboration: do you have some literature references in this regard, and could you provide me some example structures with known pitch and radius parameters? I have some general idea and need to work on some specific examples to make sure it is practical.

Thanks,

Xiang-Jun

PS. We are currently testing the new 3DNA server using this forum, and it seems pretty stable. In the near future, the 3DNA homepage will hosted here, with a new interface. We are planning to add databased driven  dynamic pages ...