Hi all, I was wondering if anyone could shed some light on what the scale factor in jiggle fit represents? Empirically, I’ve found that a value of 0.1 with 1000-10000 trials seems to work pretty well for fitting domains in cases where the initial orientation is quite far from the optimum (where rigid body fitting fails), but it would help to know what I’m playing around with.
Also, fit_molecule_to_map_by_random_jiggle and fit_chain_to_map_by_random_jiggle both seem to return 0.0 when called regardless of whether they find a better orientation - Perhaps it would be helpful for scripting purposes if they returned the new best score instead? I am using the python versions of these functions. Many thanks, Oliver.
