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

Scott Classen sclassen at lbl.gov
Thu Mar 11 14:02:53 PST 2010

OK, problem solved. Thanks to Peter Zwart.

My "original" mtz file was generated from a CNS cv file many moons ago. I must have done this conversion in such a way that the F-obs were calculated from the input IOBS (some of which were slightly negative). This resulted in the mtz file indeed having ~3200 F-obs with values of zero. It was my intention during the original conversion process to keep the FOBS values from the cv file and merely import them into the mtz.

This counts as user error.

Thanks for all the quick responses and for the A+ user support.


On Mar 11, 2010, at 1:21 PM, Pavel Afonine wrote:

> Hi Scott,
>> Can phenix.refine be directed to use F-obs <= 0?
> No. See:
> http://www.phenix-online.org/version_docs/1.6.1-336/refinement.htm
> section "Remark on using amplitudes (Fobs) vs intensities (Iobs)".
>> 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?
> It rejects reflections by sigma. In the past people used to cut the data at 2sigma or so. It is 0 by default in phenix.refine.
> Pavel.
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