Many thanks for the quick response Paul. So It scales only the translations, not the rotations? Are the test rotations systematic then, not random? What are the starting values that it scales - random between 0 and 10 Å in x,y,z for example? (Apologies for all the questions!)
Cheers, Oliver. On Mar 29, 2014, at 3:25 PM, Paul Emsley <[email protected]> wrote: > On 29/03/14 19:19, Oliver Clarke wrote: >> 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. > > jiggle_scale_factor scales the translations. By default these are 0.1 in > each of the x,y,z directions. In my scripts I use between 1 and 3. > >> >> 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. >> > > Yes it does, yes it would :) > > Paul. >
