[phenixbb] Filtering ordered solvent molecules based on secondary map
pafonine at lbl.gov
Tue Jan 4 14:34:40 PST 2011
> 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).
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb