[phenixbb] ordered solvent - parameters?

Mark Collins mcollins at convex.hhmi.columbia.edu
Thu Jul 31 14:03:40 PDT 2008

Hi All

I was just going through the .help section and website documentation
for ordered_solvent.  And wonder if somebody could enlighten me as too
the meanings of;

ordered_solvent {
     primary_map_type = mFobs-DFmodel
     secondary_map_type = 2mFobs-DFmodel
     h_bond_min_mac = 1.8
     h_bond_min_sol = 1.8
     h_bond_max = 3.2
   peak_search {
     map_next_to_model {
       use_hydrogens = False
     max_number_of_peaks = None
     peak_search {
       peak_search_level = 1
       max_peaks = 0
       interpolate = True
       min_distance_sym_equiv = None
       general_positions_only = False
       min_cross_distance = 1.8

What is the difference between the primary and secondary map?  Is there
away to pick sites in one and remove in another? Eg. pick sites at 3  
in FoFc and remove if 1.2 sigma in 2FoFc.

I thought h-bonding was generously about 2.4-3.6A so why the 1.8 and 3.2
defaults?  Also if use_hydrogens = True, does the refinement use h_bond
parameters instead of model_peak_dist and peak_peak_dist parameters, or
both? Also what do all of the peak_search parameters do?

And finally does anyone have any recommendations for progessively  
the ordered_solvent parameters?  In CNS we used to gradually lower the
2FoFc peak picking (and deleting) and increase the bfactor_max for

Thanks Mark

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