Finding non-sequential base step parameters

Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Questions and answers > General discussions (Q&As)

(1/1)

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:

--- Quote from: "Mauricio" ---I am wondering if it's possible to find all base step parameters
--- End quote ---
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.

--- Quote from: "Mauricio" ---I am aware that I can isolate the base_step and calculate the step parameters for them
--- End quote ---
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

Navigation

[0] Message Index

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.

Go to full version