Finding non-sequential base step parameters

[mauricio esguerra]

Hello Dr. Xiang-Jun,

I have been using:
find_pair -s rnastructure.pdb stdout | analyze
to obtain the .outs file which contains the sequential base step parameters for the analysed structure.
I am wondering if it's possible to find all base step parameters, including those which are non-sequential, for example, in the ribosomal structure of pdb:id 1jj2, the bases G_1709 and A_1711 stack in top of each other and therefore their step parameters can be computed, but are not given by default in rnastructure.outs.

I am aware that I can isolate the base_step and calculate the step parameters for them, but I was wondering if it's possible to do without the additional step.

Thanks once again,

Mauricio Esguerra

[xiangjun]

I am wondering if it's possible to find all base step parameters

No, it is not possible. There are simply too many possibilities, e.g., for 23S rRNA in 1jj2, and most of them make no sense at all.

I am aware that I can isolate the base_step and calculate the step parameters for them

What do you mean to "isolate the base_step"? If you separate find_pair -s from analyze, you could simply play with the output file from the former to get what you want.

HTH,

Xiang-Jun

[mauricio esguerra]

Thanks for the fast reply Dr. Xiang-jun,

What I meant by "isolate the base-step" was just that I have a script to pull out to a new structure, say residues G_1709 and A_1711 from the whole ribosomal structure 1jj2, and then I can run 3DNA on this new structure to compute the step parameters that I'm looking for.

Thank you for the advice. I just did it using your advice by separating find_pair -s from analyze, and modification of find_pair output, and it works perfect.

Thanks,

Mauricio