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Hi Andrew,<br>
<br>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"> 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?</span></p>
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<br>
yes, they should. They use the same code - that's the joy of having
libraries: multiple applications can re-use the same core routines.
<br>
<span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31, 73,
125);"><o:p> </o:p></span>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"> 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?</span></p>
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<br>
This I would need to check since I don't remember. As I hope all
phenix.refine users know, by default phenix.refine writes out two
2mFo-DFc maps (one is using original Fobs set, and one using Fobs
set where missing Fobs are filled with DFc), and one mFo-DFc map.
Most likely, for water picking phenix.refine uses the one 2mFo-DFc
map that uses original set of Fobs.<br>
<br>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"> Specifically, does phenix.refine use “filled”
maps for ordered solvent checking?</span></p>
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<br>
Unlikely.<br>
<span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31, 73,
125);"><o:p> </o:p></span>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"> 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. </span></p>
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<br>
Yes, I kind of figured this out... -:) Although I'm wondering why
you are not happy with the default settings which are supposed to be
good enough most of the time?<br>
<br>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">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.</span><br>
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<br>
I see. I think you are on the right track to achieve this. Depending
how generous you are setting the water selection criteria you can
get as many waters as you want. This is not always bad (as many
typically think) but just emulates some earlier versions of ARP idea
which is in the end is pretty successful. That is: modeling some
density peaks that you cant interpret in terms o your model right
now with "dummy waters" may improve the overall map quality which
might be helpful.<br>
<br>
Pavel.<br>
<br>
<br>
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