<div dir="ltr">Hi Christian,<div><br></div><div>Could you answer the following questions:</div><div><br></div><div>- what is the resolution of the data set?</div><div>- what is average B of the protein?</div><div>- what are the starting B values for the ligand?</div><div>- did you try lowering starting B for the ligand and repeat the refinement? Is this behavior reproducible with different refinement options?</div><div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Oct 30, 2016 at 11:06 AM, Christian Roth <span dir="ltr"><<a href="mailto:christianroth034@gmail.com" target="_blank">christianroth034@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p><font face="Arial">Hi Phenix Team,</font></p>
<p><font face="Arial">regarding that ligand issue in this thread, we
observed the same with a ligand in one of our structures now.
After refinement the ligand is surrounded by pos diff density and
the B-Factors are around 200 (way above any useful range in that
case).</font></p>
<p><font face="Arial">The cif was generated using elbow and phenix
runs with options Real space refinement, TLS on, individual B,
and optimizing weights. Nothing crazy.</font></p>
<p><font face="Arial">Could you find a solution for the previous
case and give us some tips?</font></p>
<p><font face="Arial"><br>
Cheers</font></p><span class="HOEnZb"><font color="#888888">
<p><font face="Arial"><br>
Christian</font></p></font></span><div><div class="h5">
<p><font face="Arial"><br>
</font></p>
<p><font face="Arial"><br>
</font></p>
<br>
<div class="m_-3740913058495017715moz-cite-prefix">Am 06.09.2016 um 01:44 schrieb Pavel
Afonine:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
Hi Tongqin,<br>
<br>
I second Dorothee's point that we need more information to resolve
this problem. If you still have this problem please send me inputs
files (data, model, .eff from last refinement, as well as ligand
.CIF files if any) and I will look into this once I have files.<br>
<br>
Pavel<br>
<br>
<div class="m_-3740913058495017715moz-cite-prefix">On 8/31/16 09:29, Dorothee Liebschner
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Tongqin,
<div><br>
</div>
<div>It is a bit difficult to diagnose with the information
you provided. Could you please answer the following
questions?<br>
<div><br>
</div>
<div>- Did you also try to reset the B-factors to similar
values than neighboring atoms?</div>
<div>F.ex. the average B-factor in the model could be 50
A**2, but in the ligand region, it could be lower, let's
say 20 A**2. Then the starting value using average B is
quite far from the likely B-factor of the ligand.</div>
<div><br>
</div>
<div>- What refinement strategy do you apply? How many
macro-cycles? Do you use any non-default parameters for
B-factor refinement?</div>
</div>
<div><br>
</div>
<div>- Which Phenix version are you using?</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Dorothee</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Aug 31, 2016 at 7:12 AM,
Zhou, Tongqing (NIH/VRC) [E] <span dir="ltr"><<a href="mailto:tzhou@mail.nih.gov" target="_blank">tzhou@mail.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div link="#0563C1" vlink="#954F72" lang="EN-US">
<div>
<p class="MsoNormal">Dear All,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I am refining a structure with
diffraction to 2.2A resolution and 95 % overall
completeness. Now the Rs are at 18% and 23%,
respectively. But the program failed to refine B
factors for several ligands, atoms had high B
factors while showing positive Fo-Fc map around
them. Occupancy was set to 1 and I also tried to
reset B to mean B of the whole PDB. Any of you
seeing this phenomenon? Thanks!</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Shown below is HEPES that has
high B factor and positive density around it after
refinement:<br>
</p>
</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<br>
<fieldset class="m_-3740913058495017715mimeAttachmentHeader"></fieldset>
<br>
</div></div><span class=""><pre>______________________________<wbr>_________________
phenixbb mailing list
<a class="m_-3740913058495017715moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>
<a class="m_-3740913058495017715moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/phenixbb</a>
Unsubscribe: <a class="m_-3740913058495017715moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.<wbr>org</a></pre>
</span></blockquote>
<br>
</div>
<br>______________________________<wbr>_________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.<wbr>org</a><br></blockquote></div><br></div>