[phenixbb] Filtering ordered solvent molecules based on secondary map

Andrew T. Torelli att29 at cornell.edu
Wed Jan 5 14:45:54 PST 2011


                Thanks for the helpful comments.  Do both phenix.model_vs_data and phenix.real_space_correlation produce the same values for CC that phenix.refine uses to keep/remove waters when the ordered solvent routine is used?

                Also, are the default 2mFo-DFc and mFo-DFc map coefficients output by phenix.refine (in the "_maps_coeffs.mtz" file) the same coefficients used by phenix.refine during the ordered solvent checking?  Specifically, does phenix.refine use "filled" maps for ordered solvent checking?

                If you haven't guessed, I am thinking of a way to intelligently pick values for the ordered solvent parameters such as primary_map_cutoff, poor_cc_threshold and poor_map_threshold. My idea is to first run a quick round of refinement with generous ordered solvent parameters  so that I get a model that is somewhat overpopulated with automatically-picked waters.  Then I can manually inspect the mFobs-DFmodel and 2mFobs-DFmodel maps (i.e. primary and secondary maps) and the CC values in order to decide where to select appropriate cutoffs to limit addition of spurious waters for a given model/dataset, which will differ based on map quality, resolution, etc.  So obviously I want to calculate CC values and maps in the same way phenix.refine would to judge waters so that I can "see what phenix sees" in this regard.

Thanks for your help (and I hope you made it to London...haha),

From: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> [mailto:phenixbb-bounces at phenix-online.org]<mailto:[mailto:phenixbb-bounces at phenix-online.org]> On Behalf Of Pavel Afonine
Sent: Tuesday, January 04, 2011 9:05 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Filtering ordered solvent molecules based on secondary map

                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.

Continuing while waiting for boarding... Actually, looking at map CC alone is not too informative although is definitely good. Imagine you compare two densities both having max sigma value say ridiculously small like 0.1 sigma. In this case you will still get high map CC (by high I almost arbitrarily mean something like 0.7-0.8 and up to 1). I looked into this at some point and it seems like you need to look at both - map CC and actual density values. Of course this is very resolution dependent... Also, what matters is the region where you compute map CC. Say you have a large residue where only a couple of ending atoms are misplaced (not in density). In this case the map CC computed for the whole residue will still be good, so you will never catch those couple of atoms. Therefore, it's better to compute map CC per atom, and not per residue. But there is a trick here too. It makes sense to compute map CC per atom only when the map shows atomicity, so you can more or less determine individual atoms. At resolutions like 3A and lower you see a blob of density for a residue, and computing CC per atoms doesn't really makes sense... I'm not aware of any systematic research on this subject. I guess it can be a nice a month or two long project for a student.

Good luck,
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