Messages

1

General discussions (Q&As) / Re: Calculating the angle of DNA curvature

« on: October 03, 2008, 12:44:17 am »

Hi Xiang-Jun,

Thank you for the reply. The recipes in your Nature Protocol paper are very helpful.
I have been trying to compare DNA bending angles of several, structurally related protein-DNA complexes. However, after working with 3DNA and CURVES for awhile, I noticed that the problem is complex, because these DNA have different structures, and thus it is difficult to compare bending angles between them. With your comments, I have convinced myself that even if the bending angles can be quantified in a certain way, the calculated angles would be difficult to interpret and may not have much meaning.

2

General discussions (Q&As) / Calculating the angle of DNA curvature

« on: September 25, 2008, 02:02:11 am »

Hi all.
I am trying to calculate the angle of curvature of a particular DNA.  Is this possible to do using X3DNA?  I read the recent Nature Protocol paper by Xiang-Jun Lu and Wilma Olson, which said,

"The 3DNA software also lets the user take advantage of the unique capability of Curves to find a global curvilinear helical axis and related global parameters, such as the widths and depths of the major and minor grooves, ..."

Does this imply that the angle of DNA curvature can only be calculated with Curves?  I do not know the basics behind how to calculate the angle of DNA curvature, so any help to point me towards the right direction will be greatly appreciated.