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

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Aug 28 07:07:12 PDT 2009

Hi Engin,

I'm not sure about your main question...I hope that Nat or Pavel will
answer you on that.

On the use of density-modified phases in refinement: AutoBuild expects
experimental phases in the data file, with experimental HL coefficients,
and it by default it will use those HL coefficients in refinement with an
MLHL target.

The phase probabilities from resolve statistical density modification are
pretty accurate, and not inflated, so you could use them in refinement if
you wanted to. I don't suggest it, however, because the
density-modification phase information is not fully independent of the
other information used in refinement (e.g., a flat solvent is implicit in
your refinement already, so including that through density modification is
partially redundant).

ps: I hope AutoBuild doesn't recommend using density-modified phases in
refinement, so if you could send me the text where it says that, I will
check that out!

All the best,
Tom T

>> 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?
>> Thanks,
>> Engin
>> --
>> 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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>> phenixbb at phenix-online.org
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