The main weakness in the current rendition of the program is that the persistence length, and various evaluation procedures such as the Flory solvent models must evaluated uniformly as the average over the entire sequence. In a number of cases, the variability in the persistence length contributes only minor errors to the entropy estimation of the structure. In such cases, the funnel shape of the free energy landscape can be enough to make up for these errors, however, in other cases; it may yield only partially reliable solutions. Naturally, for the most interesting RNA, there is likely to be "interesting" variability, and this may be a problem. We can only claim that this may help as a guidebook, but like a guidebook, you still have to stumble on the mineral or the animal before you have any opportunity to identify it.
For relatively short sequences of about 100 nt, assuming a fixed persistence length often appears to be a reasonable guess, however, for longer sequences, this can lead to problems. Future versions of this program will break away from the monolithic persistence length we have imposed here and are expected to be able to handle larger structures more accurately than this version can.