[phenixbb] default treatment of Intensities and structure factors in phenix.refine

fn1 at rice.edu fn1 at rice.edu
Sat Jul 14 20:12:00 PDT 2012

Does your input mtz file have both intensities and structure factors?  
If yes, you could set xray_data.labels="FP SIGFP" to ask phenix to use  
the structure factors.


Quoting Yarrow Madrona <amadrona at uci.edu>:

> Hi,
> I recently noticed from reviewing the phenix.refine log file that phenix
> is scaling the input intensities using the French-Wilson Method. However,
> I have already run Truncate in CCP4 and have structure factors in my MTZ.
> So it appears that Phenix.refine ignores structure factors and uses
> intensities regardless.
> The reason I am concerned is that Nat recently mentioned that the default
> for the sigma I cutoff is zero. However, The default in Truncate I thought
> was -3. If I understand correctly, the treatment in truncate allows weak
> reflections to be scaled and converted to structure factors. It seems that
> setting the I sigma cutoff to zero would cause you to loose some useable
> data. Currently, the sigma_fobs_rejection_criterion and
> sigma_ibos_rejection_criterion = None. This is the default I guess which
> would be 0. So my questions are:
> 1. Will setting:
> sigma_iobs_rejection_criterion = -3
> result in Phenix using a sigma I cutoff of -3?
> 2. How do I tell phenix to use the structure factors created by Truncate?
> Thanks for your help. I apologize  if I have some misconceptions as I am
> still relatively new to crystallography.
> -Yarrow
> --
> Yarrow Madrona
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
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