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: [email protected] [mailto:[email protected]] 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 [email protected]http://mailto:[email protected] Date: Wed, Dec 16, 2015 at 2:06 PM Subject: Re: [phenixbb] ML with Twinning? To: “Keller, Jacob” [email protected]http://mailto:[email protected], “[email protected]mailto:[email protected]” [email protected]http://mailto:[email protected] 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 ________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]