[phenixbb] Refinement with new mtz.file
Aleksandar Bijelic
aleksandar.bijelic at univie.ac.at
Tue Jul 22 10:01:19 PDT 2014
Am 22.07.2014 16:35, schrieb Morten Grøftehauge:
> 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 default.
>
> 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 great.
>
> Cheers,
> Morten
>
>
>
> On 22 July 2014 08:15, Aleksandar Bijelic
> <aleksandar.bijelic at univie.ac.at
> <mailto:aleksandar.bijelic at univie.ac.at>> wrote:
>
> Am 21.07.2014 19 <tel:21.07.2014%2019>: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 <tel:%2B43%201%204277%2052536>
> e-Mail: aleksandar.bijelic at univie.ac.at
> <mailto:aleksandar.bijelic at univie.ac.at>
>
> --------------------------------------------
>
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>
>
>
>
> --
> Morten K Grøftehauge, PhD
> Pohl Group
> Durham University
Thank you very much. Indeed, I started from a good search model (maybe)
explaining this low Rfree value. Unfortunately I am now confused, I
copied the Rfree flags from my old mtz.file to my new one (as described
by you), but Phenix giving me still the error saying that this flags
were already used in previous runs ..... is this usual? The funny thing
is when I change the refinement by unchecking "update water" Phenix is
running without complainig ... why? Sorry for my "stupid" questions but
in my lab there is no one who I could ask since I am the only one who is
trying to solve a structure.
Aleks
--
-------------------------------------------
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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