What values are good for persistence length? This depends strongly on the sequence you are studying. You need to understand what you are studying.
If it consumes up large quantities of Mg, is an enormously long sequences, and tends to be very stiff as a scaffold, then you should probably be thinking about a large value for you persistence length.
If, on the other hand, it is used in recognition and can easily change structure, it is probably not very stiff, and hence, you should probably be thinking about a short persistence length.
Although there may be a objective way to decide this aspect of the structure without the input of the user, it seems like the user should understand something about what he/she expects based upon some experimental information. When no such estimate can be decided clearly, the best alternative is to try to fit the structure to a range of values. For a new structure, it may be hard to know what is correct, but again, one can use the caveats given above. If it is a scaffold, then it is stiff, but if it is a segment that is used for recognition or bioactivity, it is most likely not.