I want to make a lot of purely structural alignment of pairs of very short RNA structures, from a length varying from 3 to 12 nucleotides (in every alignments both RNA structures will have the same number of nucleotides), which are supposed to have similar geometry. I tried to use cealign but the selection is too short, and I don't think that resizing the windows will give me a good alignment, super don't work because of the C alpha selection with the option seq=0, align make sequence alignment, fit take only structures of the same size.

 I really don't want to have any sequence based information in the alignment.

At the moment I didn't find a solution does anyone have one which can do the task, just  an idea will help me a lot ?

Alexis Delabriere