Messages

1

General discussions (Q&As) / Re: bending angle of DNA

« on: August 05, 2010, 02:21:51 am »

Dear Xiang-Jun,

Thanks for fast and helpful response!

Works a treat.

For R users: you should be able to get the angle with this short calculation:
(180/pi)*acos(sum(vector1*vector2))
Vector 1 and 2 you will obtain following the recipe posted by Xiang-Jun above.  
We get an angle of 72 degree for 3f27 (close to the guesstimated 80deg reported).

Cheers,

Ralf

2

General discussions (Q&As) / bending angle of DNA

« on: August 04, 2010, 10:21:20 pm »

Dear all,

We are working on Sox proteins that bind the minor groove of DNA and induce a rather drastic bend. 3DNA is of fantastic help to analyze base-pair and base step parameters. However, it's common standard to report an actual overall bending angle. It's surely possible to estimate such a bending angle from structural models and report a rough value - we have done so in the past. But I am wondering whether there is a more accurate way of defining this angle (i.e. by defining a kink point and helical axis extending from there).

Regards,

Ralf