[phenixbb] Filtering ordered solvent molecules based on secondary map

Andrew T. Torelli att29 at cornell.edu
Tue Jan 4 14:45:39 PST 2011

Thanks Pavel,

                So the default value for the poor_map_value_threshold is 1, which I assume is 1 sigma.  So if the electron density for a putative water is less than 1 sigma in the 2mFo-DFc map OR if the calculated correlation coefficient is less than the poor_cc_threshold value (default 0.7), then the water is removed, right?

                For my own education, what would be the best way of calculating the correlation coefficient values for all the waters or ligands in a given model?  What I want to do is get a sense for the relationship between electron density and correlation coefficient values for waters in my structure to understand how "strict" the default poor_cc_threshold value is and whether/how much I might want to raise it.

Thanks for your help,

From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
Sent: Tuesday, January 04, 2011 5:35 PM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Filtering ordered solvent molecules based on secondary map

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 (poor_map_value_threshold).

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


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