[phenixbb] How to change the FOBS/SIGMA_FOBS value in phenix.refine

Randy Read rjr27 at cam.ac.uk
Mon Jan 8 00:38:12 PST 2018

Dear Jianxu,

What you're seeing here is the effect of the French and Wilson algorithm to turn intensities into amplitudes.  As the SIGI gets larger and larger, the French and Wilson algorithm provides an F that becomes closer and closer to the mean amplitude in the Wilson distribution for amplitudes, and the SIGF becomes closer and closer to the rms deviation from the mean amplitude in the Wilson distribution.  As a result the minimum F/SIGF that you can possibly find is about 1.913 for acentric reflections and 1.324 for centric reflections (http://journals.iucr.org/d/issues/2016/03/00/dz5382/index.html#FD29).  The 1.35 that you see would be for a centric reflection that is close to having no information in the original intensity measurement.

Best wishes,

Randy Read

> On 8 Jan 2018, at 03:20, Pavel Afonine <PAfonine at lbl.gov> wrote:
> Hi Jianxu,
>> Is there place to set the I/SIGMA_I or FOBS/SIGMA_FOBS values in phenix.refine? I found the default FOBS/SIGMA_FOBS threshold in phenix.refine is 1.35, which means any reflection lower than 1.35 will be excluded in the refinement process. This will generally result in a lower completeness range especially for the relatively weak datasets. When I uses the xray_data.remove_outliers=False, I got the error message "Sorry: Unknown command line parameter definition: remove_outliers = False", and my PHENIX version is phenix-1.12-2829, thanks.
> phenix.refine does not remove reflections by I/SIGI or F/SIGF criteria. What you see is the file is the result of taking all Fobs, all sigmas, defining one by another, taking min of that and reporting in PDb file header.. So, 1.35 is the actual min(FOBS/SIGFOBS) for data in your file. If you want to aply such a cutoff, then use:
> xray_data.sigma_fobs_rejection_criterion=VALUE
> or
> xray_data.sigma_iobs_rejection_criterion=VALUE
> Pavel
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Randy J. Read
Department of Haematology, University of Cambridge
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