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

[Pavel Afonine]

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