[phenixbb] Fwd: ML with Twinning?

[Keller, Jacob]

There are a number of twinning tests, and if they indicate a ~>5% twin fraction, the convention is to use twin refinement. Refining twin fractions then gives a more accurate estimate of the true fraction.

I think your hypothetical about not helping anything besides R might not really happen in practice—has it happened to you, or do you know of such a case? In any case, if you know something is there in your data (twinning, waters, chloride ions, etc) why not model it if you have reasonable evidence that it’s there?

JPK

From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of wtempel
Sent: Wednesday, December 16, 2015 3:21 PM
To: PHENIX user mailing list
Subject: [phenixbb] Fwd: ML with Twinning?


Hello,
please allow me to use this prompt for my twinning-related question.
A recent version of xtriage prints this warning:

It might be worthwhile carrying out refinement with a twin specific target function.
Please note however that R-factors from twinned refinement cannot be directly
compared to R-factors without twinning, as they will always be lower when a
twin law is used. You should also use caution when interpreting the maps from
refinement, as they will have significantly more model bias.

Consider a case where specification of a twin law produces a “significant” reduction in the residuals, say between 5 and 10%-points. Maps have not revealed any additional features or model errors. Model geometry (such as fraction of residues in favored regions of the Ramachandran plot) has not improved. Should I specify the twin target during refinement?
How do my colleagues decide when to use twin refinement?
Best regards.
Wolfram Tempel

————— Forwarded message —————
From: Pavel Afonine pafonine at lbl.gov<http://mailto:pafonine@lbl.gov>
Date: Wed, Dec 16, 2015 at 2:06 PM
Subject: Re: [phenixbb] ML with Twinning?
To: “Keller, Jacob” kellerj at janelia.hhmi.org<http://mailto:kellerj@janelia.hhmi.org>, “phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>” phenixbb at phenix-online.org<http://mailto:phenixbb@phenix-online.org>

Hi Jacob,
Is Phenix able yet to use the ML target function with twinned data?

no.
Is it in the works?

There are formulas written out:

“Maximum likelihood refinement for twinned structures”:

http://phenix-online.org/newsletter/CCN_2011_01.pdf

some one needs to code it.

Pavel

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