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