[phenixbb] generate r free flags in phenix.refine not obeying high resolution limit?
pafonine at lbl.gov
Wed Aug 20 09:45:01 PDT 2008
yes - only if you have exactly matching datasets. For example one MTZ
(or any other format) file with Fobs and another MTZ (or any other
format) file with free-R flags; and the hkl indices in both files are
identical. Otherwise, no.
I'm not sure, may be Ralf or Peter have some scripts to do this - I
remember someone asked for this, but may be I'm wrong...
On 8/20/2008 9:35 AM, Michael Hothorn wrote:
> Hi Pavel,
> I'd like to add a question to this. Is there a way in phenix to inherit
> the test reflections from another reflection file i.e. in .mtz format?
> Pavel Afonine wrote:
>> Hi Francis,
>> it is always the best to generate the free R flags for the whole dataset
>> and this is what phenix.refine does (I will have to double-check,
>> though). Because, for example, if you change your mind and later decide
>> to use more data, you will run into trouble with generating free R flags
>> for the rest of reflections for which you haven't done it in the beginning.
>> Also, phenix.refine generates free R that are evenly distributed over
>> the resolution, making sure that relatively thin resolution bins receive
>> enough of reflections (to assure correct ML estimations).
>> So, I don't see any problem here... Am I missing something?
>> On 8/20/2008 8:58 AM, Francis E Reyes wrote:
>>> Hi all
>>> When generating R-Free flags from phenix refine, flags are generated
>>> all the way to the limit of the data. However, shouldn't flags be
>>> generated up to the limit of the data if specified via
>>> n ? If not, are the statistics for R/Rfree matching to high resolution
>>> data that may be suspicious ?
>>> Francis Reyes M.Sc.
>>> 215 UCB
>>> University of Colorado at Boulder
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>>> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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