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 } } } _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb