[phenixbb] does phenix.refine ignore F-obs, SIGF-obs?

Scott Classen sclassen at lbl.gov
Thu Mar 11 11:57:50 PST 2010


On Mar 11, 2010, at 10:03 AM, Pavel Afonine wrote:

> Hi Scott,
>> I have an mtz file that has:
>> I-obs
>> SIGI-obs
>> F-obs
>> SIGF-obs
>> I want phenix.refine to use F-obs and SIGF-obs, but even though I 
>> provide :
>> labels = "F-obs,SIGF-obs"
> by default phenix.refine takes I-obs,SIGI-obs. You need to tell phenix.refine explicitly that you want to use F-obs,SIGI-obs.

OK it looks like phenix.refine IS using the F-obs and SIGF-obs, but it is still rejected a couple thousand reflections that have values <= 0.

Can phenix.refine be directed to use F-obs <= 0?

in particular can either of these flags be given slight negative numbers?

input.xray_data.sigma_fobs_rejection_criterion= -0.1
input.xray_data.sigma_iobs_rejection_criterion= -0.1

BTW what does this flag do?

input.xray_data.ignore_all_zeros= True


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