[phenixbb] default treatment of Intensities and structure factors in phenix.refine
amadrona at uci.edu
Sun Jul 15 08:07:43 PDT 2012
Yes, the mtz contains both. Thank you for the tip. This seems like the simplest solution.
On Jul 14, 2012, at 8:12 PM, fn1 at rice.edu wrote:
> 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>:
>> 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
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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