Hi Oliver, phenix.refine has an option to generate free-r flags in thin shells with 20 being the default number of shells (it is a user changeable parameter). It's not exactly what you quoted below but my understanding it is meant to address this potential bias. Pavel On 7/2/13 1:32 AM, "Weiergräber, Oliver H." wrote:
Hello,
while refining a structure with NCS, I was re-considering this paper from Michael Chapman's group:
Fabiola F, Korostelev A, Chapman MS. Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry. Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):227-38.
In essence, they suggest to exclude from the working set reflections that are (1) related to a test reflection by NCS (2) adjacent to a test reflection and its NCS mates in reciprocal space
They have implemented this strategy in a CNS module (R-free2005), but the software is no longer actively supported. Does anybody know if something similar has ever been implemented in other software packages such as phenix? Or am I missing any significant downsides of the approach - apart from a reduction of the working set?
Best regards, Oliver