[phenixbb] generate r free flags in phenix.refine not obeying high resolution limit?

Pavel Afonine pafonine at lbl.gov
Wed Aug 20 09:45:01 PDT 2008


Hi Michael,

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...

Pavel.

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?
>
> thanks
> Michael
>
> 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?
>>
>> Pavel.
>>
>>
>> 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  
>>> refinement.input.xray_data.high_resolutio
>>> n ? If not, are the statistics for R/Rfree matching to high resolution  
>>> data that may be suspicious ?
>>>
>>>
>>> Thanks
>>>
>>> FR
>>>
>>> ---------------------------------------------
>>> Francis Reyes M.Sc.
>>> 215 UCB
>>> University of Colorado at Boulder
>>>
>>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>>
>>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>>
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>>>   
>>>     
>>>       
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