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Hello Smith,<br>
<br>
<blockquote
cite="mid:61917642.1644751.1421551267766.JavaMail.yahoo@jws10069.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">In the X-ray
statistics by resolution bin of the Phenix.refine result, there
is a column "%complete". �For my refinement data, I find the
better the resolution (from lower resolution to the higher
resolution), the lower the completeness (for example for 40-6 A,
%complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A,
�%complete is �6%).
<div id="yui_3_16_0_1_1421549604340_5528" class="" style=""><br
class="" style="">
</div>
<div id="yui_3_16_0_1_1421549604340_5528" class="" style="">Will
you please tell me what does this "%complete" mean? why it
decreases in the better diffraction bin?</div>
</div>
</blockquote>
<br>
Completeness is how many reflections you have compared to
theoretically possible. So the higher completeness the better.
Ideally (and it's not that uncommon these days) you should have 100%
complete data set in d_min-inf resolution. Anything below say 80 in
any resolution bin is bad, and numbers you quote 6-60% mean
something is wrong withe the dataset.<br>
<br>
<blockquote
cite="mid:61917642.1644751.1421551267766.JavaMail.yahoo@jws10069.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yui_3_16_0_1_1421549604340_5528" class="" style="">For
the Ramachandran restrain in the Phenix.refine, there was a
recommendation that for good resolution (I forget how much
exactly, maybe 2.5 A), do not use Ramachandran restrain. </div>
</div>
</blockquote>
<br>
True.<br>
<br>
<blockquote
cite="mid:61917642.1644751.1421551267766.JavaMail.yahoo@jws10069.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yui_3_16_0_1_1421549604340_5528" class="" style="">But
for a crystal data with resolution better than 1.5 A, in the
X-ray statistics by resolution bin of the Phenix.refine
result, there are more rows with resolution poorer than the
defined 2.5 A (for example 40-6 A,6-3 A), although the crystal
has a resolution better than 1.5 A (for example 1.4 A), can I
use Ramachandran restrain in the Phenix.refine in this
situation?</div>
<div id="yui_3_16_0_1_1421549604340_5528" class="" style=""><br
class="" style="">
</div>
<div id="yui_3_16_0_1_1421549604340_5528" class="" style="">If I
use Ramachandran restrain in the Phenix.refine, I find the
R-work and R-free level goes up, can we say the strategy of
Ramachandran restrain in my refinement was not appropriate?<br>
</div>
</div>
</blockquote>
<br>
A situation when using Ramachandran restraints may be useful starts
at approximately 3A resolution and lower. Also note, Ramachandran
restraints may only be used to prevent Ramachandran plot outliers,
not fix them. And if you use these restraints to fix Ramachandran
plot outliers (for example, when there are too many so that manual
fixing is not practical), then make sure all fixed outliers make
sense.<br>
<br>
Pavel<br>
<br>
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