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<div class="moz-cite-prefix">Am 22.07.2014 16:35, schrieb Morten
Grøftehauge:<br>
</div>
<blockquote
cite="mid:CAEAG6YTp08Cds8BLAQhOSc8NXOMMZGq_v=3U2d+dvtf5oH6ZNw@mail.gmail.com"
type="cite">
<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
moz-do-not-send="true"
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 moz-do-not-send="true" 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=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>
-------------------------------------------<br>
Aleksandar Bijelic, MSc.<br>
<br>
Institut für Biophysikalische Chemie<br>
Universität Wien<br>
Althanstrasse 14<br>
A-1090 Wien<br>
<br>
Tel: <a moz-do-not-send="true"
href="tel:%2B43%201%204277%2052536"
value="+431427752536" target="_blank">+43 1 4277 52536</a><br>
e-Mail: <a moz-do-not-send="true"
href="mailto:aleksandar.bijelic@univie.ac.at"
target="_blank">aleksandar.bijelic@univie.ac.at</a><br>
<br>
--------------------------------------------<br>
<br>
</div>
<div class="HOEnZb">
<div class="h5">
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Morten K Grøftehauge, PhD
<div>Pohl Group</div>
<div>Durham University</div>
</div>
</blockquote>
<br>
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. <br>
<br>
Aleks<br>
<pre class="moz-signature" cols="72">--
-------------------------------------------
Aleksandar Bijelic, MSc.
Institut für Biophysikalische Chemie
Universität Wien
Althanstrasse 14
A-1090 Wien
Tel: +43 1 4277 52536
e-Mail: <a class="moz-txt-link-abbreviated" href="mailto:aleksandar.bijelic@univie.ac.at">aleksandar.bijelic@univie.ac.at</a>
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