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

Yes, the mtz contains both. Thank you for the tip. This seems like the simplest solution. Yarrow On Jul 14, 2012, at 8:12 PM, [email protected] 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.

fengyun

Quoting Yarrow Madrona :

...

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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb