<div dir="ltr">Go to "Reflection Tools" and open "Reflection file editor". <div>Add the two files, the one you want your Rfree flags from and the one with your new reflections. </div><div>Scroll down and click "Copy all arrays". Now delete the ones you don't want in the output arrays. </div>
<div>Go to the "Output options" tab. "Extend existing..." should be ticked by default. </div><div><br></div><div>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. </div>
<div><br></div><div>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). </div>
<div><br></div><div>And yes, data processing has improved immensely in later years. AIMLESS is great. </div><div><br></div><div>Cheers,</div><div>Morten </div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 22 July 2014 08:15, Aleksandar Bijelic <span dir="ltr"><<a href="mailto:aleksandar.bijelic@univie.ac.at" target="_blank">aleksandar.bijelic@univie.ac.at</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Am <a href="tel:21.07.2014%2019" value="+12107201419" target="_blank">21.07.2014 19</a>:26, schrieb Dale Tronrud:<div><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Certainly the replacement of the free flags with novel values will<br>
explain the observation that the "free R" became about equal to the<br>
working R, but it does not explain the sharp drop in the working R when<br>
you switched to the new version of you observations. This change is<br>
hard to understand without some details of your "optimizing and<br>
polishing". Did you end up with about the same number of "unique<br>
reflections"? This result is possible if you discarded a bunch of your<br>
weal, poorly estimated, reflections and the new data set had a lower<br>
completeness. Without details this is pure speculation.<br>
<br>
Dale Tronrud<br>
<br>
On 07/21/2014 07:55 AM, Pavel Afonine wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Aleksandar,<br>
<br>
the answer is in your statement:<br>
<br>
"""<br>
In the sake of completeness, I deleted the header of the used pdb.file<br>
because of the R-flag error which occurs, since Phenix reconizes that<br>
the pdb.file was already used with other Rflags.<br>
"""<br>
<br>
meaning that Rfree flags in new and old files are not consistent. In<br>
turn, this means comparing R-factors in this case is nonsensical. Once<br>
you switched to the new file simple forget about previous one along with<br>
corresponding R-factors. Of course in new file free-r reflections are<br>
not fully free, so you need to remove memory from them by running some<br>
refinement.<br>
<br>
May be a cleaner way is to transfer free-r flags from old to new file,<br>
and then new flags for portions of new reflections that do not match the<br>
old one. Again, R-factors will not be comparable between refinements<br>
against old and new files.<br>
<br>
Pavel<br>
<br>
On 7/21/14, 5:32 AM, Aleksandar Bijelic wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear CCP4 user and experts,<br>
<br>
I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24<br>
(with good geometry according to Ramachandran, Beta Outliers, etc.)<br>
.... Everything seems to be ok (especially in relation to the<br>
resolution) .... because the mtz.file I used was quite old and I<br>
cannot find my xscale.hkl file, I processed the data set again (this<br>
time with optimizng and polishing) and received a "better" file<br>
according to almost everything (resolution limit, I/sigma, CC(1/2),<br>
Rmeas), thus I used this new mtz.file and put it in my last refinement<br>
step (the refinement which led to the above mentioned Rfree = 0.24).<br>
Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19<br>
but ending up with 0.20 and 0.22, respectively. So I wanted to know if<br>
this is usual? I was expecting my data to become slightlly better but<br>
what is irritating me is the starting R-values of the refinement and<br>
that it get worse during refinement. Maybe I did something wrong? Is<br>
it reasonable to replace the mtz.file with a new one in the last<br>
refinement step or should I start the refinement from the scratch? In<br>
the sake of completeness, I deleted the header of the used pdb.file<br>
because of the R-flag error which occurs, since Phenix reconizes that<br>
the pdb.file was already used with other Rflags. Sorry, but I am still<br>
a beginner in this field, so I would be very grateful if somebody<br>
could explain me this situation and my mistake and if I need to start<br>
refinement from the beginning. Thank you in advance!<br>
<br>
Best Regards.<br>
<br>
Aleksandar<br>
<br>
</blockquote>
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<br></div></div>
Thank you for your response,<br>
<br>
@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.<br>
<br>
@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=<u></u>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.<br>
<br>
<br>
Best Regards,<div class="im HOEnZb"><br>
<br>
Aleksandar<br>
<br>
-- <br>
------------------------------<u></u>-------------<br>
Aleksandar Bijelic, MSc.<br>
<br>
Institut für Biophysikalische Chemie<br>
Universität Wien<br>
Althanstrasse 14<br>
A-1090 Wien<br>
<br>
Tel: <a href="tel:%2B43%201%204277%2052536" value="+431427752536" target="_blank">+43 1 4277 52536</a><br>
e-Mail: <a href="mailto:aleksandar.bijelic@univie.ac.at" target="_blank">aleksandar.bijelic@univie.ac.<u></u>at</a><br>
<br>
------------------------------<u></u>--------------<br>
<br></div><div class="HOEnZb"><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Morten K Grøftehauge, PhD <div>Pohl Group</div><div>Durham University</div>
</div>