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.
