I have been running through the examples in the Fiser and Sali paper
concerning the modeling of the loop in cpCN-V (circularly permuted
cyanovirin). I used the given scripts, modifying it to allow the
modeling of different linker lengths, from 6 to 12 residues, as
suggested in the paper. 200 final models of each linker were obtained,
the model with the lowest energy score (objective function) being
selected in each case. This gave the following table of results:
Length (aa) Residues Objective Function Model # File Name