[phenixbb] Filtering ordered solvent molecules based on secondary map

Pavel Afonine pafonine at lbl.gov
Tue Jan 4 14:34:40 PST 2011

  Hi Andy,

>                 I'm looking for a description of how the 
> "secondary_map_and_map_cc_filter" parameter operates.  The default is 
> set to be a 2mFobs-DFmodel, and I assume it's calculating a 
> correlation coefficient as the basis for filtering waters that are 
> present in the mFobs-DFmodel maps (i.e. primary map) but not in the 
> 2mFo-DFc map.  However, I'd like to confirm my assumption is true and 
> also learn whether the cutoff value for whether or not a putative 
> water molecule gets culled can be changed.  I haven't found the 
> information in the online documentation or the Phenixbb archives.

yes, the second map, 2mFo-DFc is used to computed map CC 
(poor_cc_threshold). Also, it is used to filter waters by the absolute 
value of the 2mFo-DFc map computed at water oxygen center 

The default values are good for most of cases (I hope).


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