[phenixbb] Refinement with new mtz.file

Aleksandar Bijelic aleksandar.bijelic at univie.ac.at
Tue Jul 22 00:15:08 PDT 2014

Am 21.07.2014 19:26, schrieb 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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Thank you for your response,

@Pavel:  I would prefer to transfer the old flags to my new reflection 
file because then I can check if my new data is indeed better. But as I 
am a less experienced user I do dnot know how to transfer Rfree flags 
.... Can I do this with the reflection file editor? And how I can get 
new R-flags for new reflections? A long time ago I read that XPLORE can 
be used for this reason, but then I have to convert my reflection file 
to "XPLORE" file and then back to mtz or I am totally wrong? I would be 
very grateful if you could explain me a method how to do this or a 
program .... maybe it is very easy but as I already mentioned I am a 
beginner in this field ... thank you in advance.

@Dale: I ended up with 56884  unique reflections (compl. 98.55%) for my 
new file. In comaprison my old file ended up with just 36075 unique 
reflections (compl. 99.75%). Thus, there is a big difference. 
Optimization and polishing means that I tried recommended procedures 
like re-integrating with the correct space group and refined geometry, 
using refined beam divergence values and comparing 
reflactions (images) for my new file because the data became worse at a 
certain image no. (due to radiation damage). This was not done with my 
old mtz.file, since I processed it by myself without any knowledge.

Best Regards,


Aleksandar Bijelic, MSc.

Institut für Biophysikalische Chemie
Universität Wien
Althanstrasse 14
A-1090 Wien

Tel: +43 1 4277 52536
e-Mail: aleksandar.bijelic at univie.ac.at


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