[phenixbb] ordered solvent - parameters?

Pavel Afonine PAfonine at lbl.gov
Thu Jul 31 16:13:17 PDT 2008

Hi Mark,

phenix.refine finds potential water peaks looking at mFo-DFc map 
(primary map). Then it sorts these peaks by the distances (water-water, 
water-other). Then it checks for hydrogen bonding. Finally, it verifies 
that the peaks are present at 2mFo-DFc map (secondary map) at given 
sigma. Finally finally, the water B-factors (and occupancies, if 
requested) are refined separately from refinement of other parameters in 
order to get a reasonable starting point for the next refinement 
macro-cycle. The procedure is smart enough about cases when your 
structure has explicit hydrogen atoms.

What is crucial is that this procedure is built into refinement, so the 
water molecules are updated (added / removed / refined) during 
refinement and NOT as a separate step.

There are various options to refine water with isotropic or anisotropic 
B-factors, refine water occupancies, etc.

We still need to do a better job on NOT picking water into ligand 
density. This is in our to-do list and will be done at some point.

There are a few slides in one of the most recent phenix.refine 
presentation that outline most of what I wrote above:


Please let us know if you have any other questions,

On 7/31/2008 2:03 PM, Mark Collins wrote:
> 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 sigma
> 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 changing
> the ordered_solvent parameters?  In CNS we used to gradually lower the
> 2FoFc peak picking (and deleting) and increase the bfactor_max for
> deleting?
> Thanks Mark
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