parameters to define quasi-continuous helix

[yrxin]

Hi Xiangjun,

I have a question about quasi-continuous helix. How does 3DNA define a "helix"? I found a couple of parameters, but was wondering if there is any other parameters. I am listing the parameters I found and some brief explanation. Please correct me and add more parameters if any.

1. helix_break: the distance between origins of two base pairs
2. std_curved: to decide if the helix is curved. (what does it mean?)

Thank you very much,

Yurong

[xiangjun]

Hi Yurong,

3DNA uses a set of simple, pure geometric criteria, for locating all possible base-pairs and double helical regions. The helical regions are defined from a base-stacking prospective, thus continuous and quasi-continuous (or no backbone at all) helices are handled in exactly the same way. The detailed underlying algorithm will become clear when I find time to write a paper on it and get the work published. Before that happens, you can simply acknowledge 3DNA for your helical region findings.

Among the two parameters you listed (which are made explicit in 3DNA v2.0 to be released soon -- following a new publication on 3DNA), only "helix_break" is relevant here. The other one is a criterion to decide if the analyzed structure is strongly curved. It is used to decide if to ls-fit a helical axis, as shown in section "Global linear helical axis defined ...", and to calculate a set of global parameters.

HTH,

Xiang-Jun