Am 21.07.2014 19:26, schrieb Dale Tronrud:Thank you for your response,
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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@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@univie.ac.at
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