[phenixbb] loosening constraints on water addition
Pavel Afonine
pafonine at lbl.gov
Thu Dec 15 09:20:58 PST 2011
Hi Crystal,
the default water selection criteria are relatively loose, although
given their amount they act pretty efficiently. Loosening them further
generates a risk of adding wrong waters. Anyway, answering your
question, here are the parameters that you can change to add more water:
ordered_solvent {
primary_map_type = mFobs-DFmodel
primary_map_cutoff = 3.0 #<<< decrease it to find more 'water'
secondary_map_and_map_cc_filter {
poor_cc_threshold = 0.7 #<<< decrease it to find more 'water'
poor_map_value_threshold = 1.0 #<<< decrease it to find more 'water'
}
h_bond_min_mac = 1.8 #<<< decrease it to find more 'water'
h_bond_min_sol = 1.8 #<<< decrease it to find more 'water'
h_bond_max = 3.2 #<<< increase it to find more 'water'
b_iso_max = 80.0 #<<< increase it to find more 'water'
}
peak_search {
map_next_to_model {
min_model_peak_dist = 1.8 #<<< decrease it to find more 'water'
max_model_peak_dist = 6.0 #<<< increase it to find more 'water'
min_peak_peak_dist = 1.8 #<<< decrease it to find more 'water'
}
max_number_of_peaks = None
peak_search {
min_cross_distance = 1.8 #<<< decrease it to find more 'water'
}
}
Pavel
On 12/15/11 9:11 AM, Crystal VanderZanden wrote:
> I'm trying to adjust the parameters on the water picking to allow for
> more waters to be found. I tried creating a solvent.params file with
> the code below, then I increased and decreased the primary map cutoff.
> When I ran the water picking command with the solvent.params file, it
> actually decreased the number of waters found, both at the high and
> low primary map cutoff. Does anyone know what I can do to relax the
> water finding criteria so more waters will be found?
>
> Thanks,
> Crystal
>
> refinement {
> ordered_solvent {
> low_resolution = 2.8
> b_iso_min = 1.0
> b_iso_max = 50.0
> b_iso = 25.0
> primary_map_type = mFobs-DFmodel
> primary_map_cutoff = 3.0
> secondary_map_and_map_cc_filter
> {
> cc_map_2_type = 2mFobs-DFmodel
> }
> }
> peak_search {
> map_next_to_model {
> min_model_peak_dist = 1.8
> max_model_peak_dist = 6.0
> min_peak_peak_dist = 1.8
> }
> }
> }
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