[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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