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Hi Igor,<br>
<br>
please make sure to try the same refinement using the latest Phenix
version from nightly builds first:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/download/nightly_builds.cgi">http://phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
The latest I see here is 1.19rc7-4070.<br>
<br>
Chances are the version you used had a bug that we fixed by now.<br>
<br>
If the problem persists please go ahead and send me inputs and
indicate residues that are bad and I will investigate right away!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/3/20 08:42, Igor Petrik wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CA+QNS+K2U7MYjpkXbPKE3UT8Jhvqd=uKmcJ7NDT4bDHBv2CMMA@mail.gmail.com">
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<div dir="ltr">
<div>Thanks Nigel,</div>
<div><br>
</div>
<div>I will put together the input and output file from my
latest refinement and send them to you and Pavel later today.<br>
</div>
<div><br>
</div>
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>- Igor Petrik<span>, PhD</span></div>
</div>
</div>
</div>
<br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Dec 2, 2020 at 9:46 PM
Folmer Fredslund <<a href="mailto:folmerf@gmail.com"
moz-do-not-send="true">folmerf@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="auto">Dear Igor
<div dir="auto"><br>
</div>
<div dir="auto">There's a phenix bulletin board for question
like this, which is where you should post the question. (
I crosspost here)</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
<div dir="auto">I would choose to not do the real space
refinement in phenix.refine during the last rounds of
refinement of a model, when sidechain positions are
essentially correct. </div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
<div dir="auto">I hope this helps</div>
<div dir="auto"><br>
</div>
<div dir="auto">Folmer</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">tor. 3. dec. 2020 05.48
skrev Igor Petrik <<a
href="mailto:petrik1@illinois.edu" target="_blank"
moz-do-not-send="true">petrik1@illinois.edu</a>>:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>I am refining a 1.71A X-ray structure with phenix
refine. I have everything modelled in - ~150 residues
in the ASU and a heme - and my R-work/R-free is
0.17/0.22. But when I went to deposit it, PDB pointed
out that two of my sidechains have distorted
geometries. One is a His, and looking at it in Coot, I
can clearly see the 2Fo-Fc density for the correct
geometry, but the actual coordinates that phenix
refine produce don't lie in that density; there are
significant difference map peaks showing that the
coordinates are in the wrong place. If I use real
space refine in Coot to put the coordinates back into
the correct density and refine it again in phenix,
they get distorted again.</div>
<div><br>
</div>
<div>What settings in phenix should I check to try to
get it to properly refine the coordinates?<br>
</div>
<div><br>
</div>
<div>Thanks,</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>- Igor Petrik<span>, PhD</span></div>
</div>
</div>
</div>
</div>
<br>
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