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 ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
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
On Tue, Jul 2, 2013 at 8:07 AM, Pavel Afonine
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.
...but doesn't do a very good job of it, based on what Randy and Paul have said in the past. -Nat
participants (3)
-
"Weiergräber, Oliver H." -
Nathaniel Echols -
Pavel Afonine