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

Yarrow Madrona amadrona at uci.edu
Sat Jul 14 20:01:23 PDT 2012


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 Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

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