How to include dotted line along helical axis in figure?

[drboer]

Dear all,

I'd like to add the helical axis as a dotted line in the 3dna-generated figures. Despite searching for it in NP08 and in the forums and website, I couldn't find how to do it.  I did see that the  stack2img help message mentions  a LISTFILE (LISTFILE  pairs of atom serial numbers for drawing a dotted line), but I can't find the format for this file, nor how to provide it to stack2img on the command line.

Any help would be highly appreciated,
Thanks in advance,
Roeland Boer.

[xiangjun]

Could you be specific on what you mean by adding "the helical axis as a dotted line in the 3dna-generated figures"? As always, a concrete example would help clarify your point.

Fig. 3 (recipe #2) of the 3DNA NP08 paper shows a dotted line contacting bp centers, but I sense that's not what you want. Does the thread "defining a local helix axis" help?

Xiang-Jun