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R-factors: Difference between revisions
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* (R<sub>sym</sub> / R<sub>merge</sub> ) should not be used to judge [[data quality]], R<sub>meas</sub> should be used instead. The reason is that the former depend on multiplicity, whereas the latter doesn't. | * (R<sub>sym</sub> / R<sub>merge</sub> ) should not be used to judge [[data quality]], R<sub>meas</sub> should be used instead. The reason is that the former depend on multiplicity, whereas the latter doesn't. | ||
* R/R<sub>free</sub> and NCS: reflections in work and test set are not independent if chosen randomly. It is better to choose the test set reflections in thin resolution shells. Since the twin related reflections have the same sin(theta)/lambda values they will not be split over the working and reference sets. [http://xray.bmc.uu.se/usf/dataman_man.html DATAMAN] from the [http://xray.bmc.uu.se/usf/ Uppsala Software Factory] and [[XPREP]] (a program which may be obtained from Bruker) offer this option. A disadvantage is the the maps may not be quite as good as when the free R reflections are selected | * R/R<sub>free</sub> and NCS: reflections in work and test set are not independent if chosen randomly. It is better to choose the test set reflections in thin resolution shells. Since the twin related reflections have the same sin(theta)/lambda values they will not be split over the working and reference sets. [http://xray.bmc.uu.se/usf/dataman_man.html DATAMAN] from the [http://xray.bmc.uu.se/usf/ Uppsala Software Factory] and [[XPREP]] (a program which may be obtained from Bruker) offer this option. The "RFREE SHELL" command in sftools is another way to select thin shells. A disadvantage is the the maps may not be quite as good as when the free R reflections are selected randomly. (FIXME: which [[Phenix]] program does this?). A paper investigating this thoroughly is Fabiola, F., A. Korostelev, et al. (2006). "Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry." Acta Cryst. D 62: 227-38. | ||
* Sets of reflections used for calculating R<sub>free</sub> should be maintained throughout a project. This is nicely discussed at http://www.bmsc.washington.edu/people/merritt/xplor/rfree_example.html . | * Sets of reflections used for calculating R<sub>free</sub> should be maintained throughout a project. This is nicely discussed at http://www.bmsc.washington.edu/people/merritt/xplor/rfree_example.html . Note that none of the programs mentioned for selecting thin shells will allow you to extend the set of shells to higher resolution if you want to preserve your existing R-free set. | ||
==Notes== | ==Notes== | ||
<references/> | <references/> | ||