I am using the ViennaRNA package. I know how to find the Minimum Free Energy structure (MFE) of a sequence using the RNAfold method. This gives me the probability of the MFE structure among all structures of that sequence. Do you know if the program is capable of computing the probability of an arbitrary structure for a given sequence? In principle, since it computes the partition function, it should be able to compute the probability of any structure within the ensemble. I just don't know how to compute the partition function for a given sequence.
Any help is highly appreciated.