[phenixbb] reflection file utility and use of modified phases in refinement

Engin Ozkan eozkan at stanford.edu
Thu Aug 27 20:59:25 PDT 2009

Hi everybody,

I had some trouble with the reflection file utility today. I've been 
trying to import Rfree-flag column from one of the mtz's to my combined 
mtz, and it never does. The R-free flag is always left out of the output 
even when I have it selected. Have you guys seen this (I'm using 147)?

Another question I have is about the output of phenix.autobuild. 
Phenix.autobuild tells me to use modified phase probabilities (HLAM, 
etc.) in refinement. I am assuming this is density-modified phases. But 
I've always thought that this would be bad practice (possibly because of 
unrealistically high FOMs and possible flattening of loops, etc, but 
maybe resolve does a better job than, say DM). Any ideas on that one?



Engin Özkan
Post-doctoral Scholar
Dept of Molecular and Cellular Physiology
Howard Hughes Medical Institute
Stanford University School of Medicine
ph: (650)-498-7111

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