Messages

1

General discussions (Q&As) / Re: defining a local helix axis

« on: July 09, 2009, 02:32:15 pm »

Thanks Xiang-Jun,

I simply put the base-pair origin coordinates (Ox,Oy,Oz) into a pdb file and diplayed those in Pymol along with the DNA coordinates. The origin coordinates do suggest regions of kinking but I will go back and also verify this with Curves and also with reference to the roll angles as you suggest.

Thanks again,
Mark

2

General discussions (Q&As) / defining a local helix axis

« on: July 08, 2009, 01:23:01 pm »

I am analyzing a protein-DNA complex in which the DNA is somewhat underwound and may have several small kinks. I wanted to calculate the helical trajectory along the DNA helix and wondered if I could use 3DNA to do this. 3DNA output gives coordinates for the origin of each base pair (Ox,Oy,Oz) as well as coordinates for the position (Px,Py,Pz) for each dinucleotide step. Would one or the other of these coordinate sets be more appropriate to use, or are neither of these a good measure of the helix axis?

Thanks!