[phenixbb] question about reflection file tools behavior

Michael Thompson miket at chem.ucla.edu
Fri Mar 1 12:43:09 PST 2013

Hello All,

I have a question about the behavior of the reflection file tools within the PHENIX GUI:

I am trying to simply copy a set of FreeRFlags from a higher resolution dataset to a lower resolution dataset. The low-res dataset contains 35264 reflections in the original input mtz. The high-res set contains 43731 reflections. When I use the GUI to write a new mtz using the low-res amplitudes and the high-res FreeRFlags, the result is an mtz with 46323 reflections. I am confused about why the output has so many reflections, even more than the high res dataset? Also, I noticed that while both input mtz files have a low-res cutoff of 20A, the output mtz has a low-res cutoff around 75A. Can anyone please explain what is going on here? I would like my output file to have the same reflections as the input, and no more. 

I have noticed that the CCP4 program FreeRFlag seems to behave in a similar way, so my guess is that what is happening is a common procedure, but I'm at a loss for an explanation of why this is the case. Also, if there's a better way to implement what I am trying to do I'd be grateful to hear it (perhaps generate entirely new flags for both datasets using the same random seed?).

Thanks for the help!!


Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

miket at chem.ucla.edu

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