[phenixbb] Refinement with new mtz.file

Morten Grøftehauge mortengroftehauge.work at gmail.com
Tue Jul 22 07:35:19 PDT 2014

Go to "Reflection Tools" and open "Reflection file editor".
Add the two files, the one you want your Rfree flags from and the one with
your new reflections.
Scroll down and click "Copy all arrays". Now delete the ones you don't want
in the output arrays.
Go to the "Output options" tab. "Extend existing..." should be ticked by

Now, since you have almost doubled your number of reflections you are still
heavily biased on the Rfree. There will probably be a heap of people who
disagree but I think the best way to use a simple simulated annealing. It
takes a while but you get a bunch of rounds of random noise + refinement.

And you will probably end up with a slightly higher Rfree. I think 24% is
very low for 3 Å data but then you have a large unit cell and probably a
very high NCS. Possibly started from some very good search models. If you
have a complex and one component is structure determined at a better
resolution then you can use that as restraint (constraint? I can never
remember the difference).

And yes, data processing has improved immensely in later years. AIMLESS is


On 22 July 2014 08:15, Aleksandar Bijelic <aleksandar.bijelic at univie.ac.at>

> 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 STRICT_ABSORPTION_CORRECTION=TRUE with
> =FALSE. Indeed, I discarded some 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
> --
> -------------------------------------------
> 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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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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