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

Jeff Headd jjheadd at lbl.gov
Sat Jul 14 20:21:59 PDT 2012

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.


On Sat, Jul 14, 2012 at 8:01 PM, Yarrow Madrona <amadrona at uci.edu> 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120714/6de4fbf5/attachment.htm>

More information about the phenixbb mailing list