Hello, when refining a protein structure against a low-resolution dataset (5 A), I wanted to also attempt real-space refinement. However, in the log file I find: |-real space refinement (target=simple)---------------------------------------| rejected... | | | --------------------------------------------------------------------------- | Changing the target to, e.g., diff_map does not change anything; the message will still refer to the "simple" target. I guess this is due to an internal resolution limit, but that's only speculation since it seems to be undocumented. Indeed, there is probably not much to be gained by real-space refinement at this resolution (at least not in terms of side-chain conformations), but I wanted to give it a try anyway. Any comments on this issue? 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 tries real-space refinement and if it increases R-factors above a certain threshold it rejects the result. You can't change this behavior it at present. This will change once a new real-space refinement is in place (which will work well at any resolution, including very low). Pavel On 3/26/13 2:00 AM, "Weiergräber, Oliver H." wrote:
Hello,
when refining a protein structure against a low-resolution dataset (5 A), I wanted to also attempt real-space refinement. However, in the log file I find:
|-real space refinement (target=simple)---------------------------------------| rejected... | | | --------------------------------------------------------------------------- |
Changing the target to, e.g., diff_map does not change anything; the message will still refer to the "simple" target. I guess this is due to an internal resolution limit, but that's only speculation since it seems to be undocumented. Indeed, there is probably not much to be gained by real-space refinement at this resolution (at least not in terms of side-chain conformations), but I wanted to give it a try anyway.
Any comments on this issue?
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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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"Weiergräber, Oliver H." -
Pavel Afonine