[phenixbb] Refinement with new mtz.file

[Dale Tronrud]

   Certainly the replacement of the free flags with novel values will
explain the observation that the "free R" became about equal to the
working R, but it does not explain the sharp drop in the working R when
you switched to the new version of you observations.  This change is
hard to understand without some details of your "optimizing and
polishing".  Did you end up with about the same number of "unique
reflections"?  This result is possible if you discarded a bunch of your
weal, poorly estimated, reflections and the new data set had a lower
completeness.  Without details this is pure speculation.

Dale Tronrud

On 07/21/2014 07:55 AM, Pavel Afonine wrote:
> Hi Aleksandar,
> 
> the answer is in your statement:
> 
> """
> In the sake of completeness, I deleted the header of the used pdb.file
> because of the R-flag error which occurs, since Phenix reconizes that
> the pdb.file was already used with other Rflags.
> """
> 
> meaning that Rfree flags in new and old files are not consistent. In
> turn, this means comparing R-factors in this case is nonsensical. Once
> you switched to the new file simple forget about previous one along with
> corresponding R-factors. Of course in new file free-r reflections are
> not fully free, so you need to remove memory from them by running some
> refinement.
> 
> May be a cleaner way is to transfer free-r flags from old to new file,
> and then new flags for portions of new reflections that do not match the
> old one. Again, R-factors will not be comparable between refinements
> against old and new files.
> 
> Pavel
> 
> On 7/21/14, 5:32 AM, Aleksandar Bijelic wrote:
>> Dear CCP4 user and experts,
>>
>> I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24
>> (with good geometry according to Ramachandran, Beta Outliers, etc.)
>> .... Everything seems to be ok (especially in relation to the
>> resolution) .... because the mtz.file I used was quite old and I
>> cannot find my xscale.hkl file, I processed the data set again (this
>> time with optimizng and polishing) and received a "better" file
>> according to almost everything (resolution limit, I/sigma, CC(1/2),
>> Rmeas), thus I used this new mtz.file and put it in my last refinement
>> step (the refinement which led to the above mentioned Rfree = 0.24).
>> Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19
>> but ending up with 0.20 and 0.22, respectively. So I wanted to know if
>> this is usual? I was expecting my data to become slightlly better but
>> what is irritating me is the starting R-values of the refinement and
>> that it get worse during refinement. Maybe I did something wrong? Is
>> it reasonable to replace the mtz.file with a new one in the last
>> refinement step or should I start the refinement from the scratch? In
>> the sake of completeness, I deleted the header of the used pdb.file
>> because of the R-flag error which occurs, since Phenix reconizes that
>> the pdb.file was already used with other Rflags. Sorry, but I am still
>> a beginner in this field, so I would be very grateful if somebody
>> could explain me this situation and my mistake and if I need to start
>> refinement from the beginning. Thank you in advance!
>>
>> Best Regards.
>>
>> Aleksandar
>>
> 
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