Hi Yarrow,

Sorry for the confusion. If input intensities are used, then the French-Wilson method is used by default. If sigma_iobs_rejection_criteria is set to None as it is by default, then internally phenix.refine will set this value to -4 when using the F&W method. Having the value set to None by default allows us to use the sigma_iobs_rejection_criteria variable for both the F&W method and the old, simpler method, but each method needs a different default value, so the idea was to leave this is an internally determined parameter unless the user had good reason to change it otherwise.

I think we need to make this more clear. I'll see about adding a message to the log file that this change has occurred internally.

Since you've already used Truncate, you can tell phenix.refine to use your amplitude arrays as Fengyun suggested, or you can remove the intensity arrays from your input .mtz entirely using the reflection file editor.

Jeff

On Sat, Jul 14, 2012 at 8:01 PM, Yarrow Madrona <[email protected]> wrote:

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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