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Hi Michal,<br>
<br>
thanks for the info! Yes, there was a bug at some point that we
fixed right after we discovered it. So it's best to use the latest
version from nightly builds.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/3/20 09:19, Boniecki, Michal
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:5f944b91-4f62-7350-e2e6-f3427f9169ee@usask.ca">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<p>I had similar case with Tyr side chain, but after installing
latest upgrades worked fine</p>
<p>Michal</p>
<br>
<div class="moz-cite-prefix">On 12/3/20 11:16 AM, Pavel Afonine
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:ed580338-80d9-b3d6-57e0-40fa24ef50d4@lbl.gov">
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<br>
<div>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"
moz-do-not-send="true">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">
<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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