[phenixbb] Refinement with new mtz.file

[Pavel Afonine]

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
>