More than one helical region

[spreus]

Hi

I'm trying to rebuild pdb structures using the information optained from the 3DNA analysis output file. For structures containing more than one helical region, e.g. two different helices separated in space, I can't find a way to extract all the information regarding the relative position and orientation of the two helices relative to one another. I've attached the output file of pdb 1NNE as an example of two different helices separated by a kink between bp 11 and 12 - of which I would like to reconstruct the nucleic acid part.

The problem is that, as far as I can tell, the 3DNA output file only contains information about the origin (Ox, Oy, Oz) and the normal vector (Nx, Ny, Nz) of all base-pairs in the coordinate system of the given structure. However, the normal vector alone is insufficient to describe the exact orientation of the base pair which requires an additional axis in the bp ref frame to be specified, e.g. the local y-axis or the x-axis in addition to the bp z-axis.

My question then is: Is it possible using 3DNA to extract all the info required to rebuild a structure consisting of more than one helical region?

Best,
Søren

[xiangjun]

Hi Søren,

I do not quite get what you mean. The "information about the origin (Ox, Oy, Oz) and the normal vector (Nx, Ny, Nz)" is not intended for rebuilding purpose, but for quantifying DNA curvature following Dickerson (FreeHelix, and related publications). The output file 'ref_frames.dat' contains all base pair reference frames in the original coordinate system. File 'bp_step.par' is used for rebuilding purpose, which should give an exact relative bp geometry, even with more than one helical fragment.

Or do you miss the "-c" option of "analyze"? Type [mono:12seu325]analyze -h[/mono:12seu325] for more info.

Please clarify.

Xiang-Jun

[spreus]

Hi Xiang-Jun

Thank you for clarifying. The ref_frames.dat file is exactly what I was looking for.

Best,
Søren