<div dir="ltr"><div>Thanks for the advice Pavel!<br><br></div>I don't want to celebrate prematurely, but I just re-ran the same refinement in both the stable and in nightly 4070, and it _seems_ to be corrected in the nightly. Will let you know if it pops up again.<br></div><div dir="auto">On Thu, Dec 3, 2020 at 9:16 AM Pavel Afonine <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>> wrote:<br></div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<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 href="http://phenix-online.org/download/nightly_builds.cgi" target="_blank">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</div><div><br>
<br>
<div>On 12/3/20 08:42, Igor Petrik wrote:<br>
</div>
</div><div><blockquote type="cite"></blockquote></div><div><blockquote type="cite">
<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">
<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" target="_blank">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">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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