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Hi Christian,<br>
<br>
somehow this escaped my attention... so was this solved in the end?
If not please send me files and I will find a solution.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 10/31/16 10:55, Christian Roth
wrote:<br>
</div>
<blockquote
cite="mid:1b6c7433-017e-0923-2eeb-329b30d7d818@gmail.com"
type="cite">
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<p><font face="Arial">Not more than 5 I'm afraid. I don't know if
it would find the right B's using 10 cycles and more, but that
also increases the running time quite considerably even on
some of our faster machines.</font></p>
<p><font face="Arial">Best wishes <br>
</font></p>
<p><font face="Arial">Christian<br>
</font></p>
<br>
<div class="moz-cite-prefix">Am 31.10.2016 um 16:46 schrieb
Dorothee Liebschner:<br>
</div>
<blockquote
cite="mid:CAAA+Ob=d-Y__9M-xR5A0sBfhmTwwrBqFsXPMmVCmUq2yvjWRbg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Christian,
<div><br>
</div>
<div>OK, it looks you found a way to prevent the positive
density by using "realistic" starting B values (of the order
of that of surrounding protein atoms).�</div>
<div>Did you also try to increase the number of macro-cycles?</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 Mon, Oct 31, 2016 at 9:11 AM,
Christian Roth <span dir="ltr"><<a
moz-do-not-send="true"
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 Dorothee</font></p>
<p><font face="Arial">to answer your questions</font></p>
<p><font face="Arial">The resolution is about 2.0 Ang
and the average B around 55. The Bfactor from the
ligand was set to the default of 20 by Coot when
placing the ligands.</font></p>
<p><font face="Arial">It seems that setting the B-value
to the average B of the structure nearly solves the
problem (most of the ligand fine, just parts with
unusuallly high values). Setting it to a bit higher
values 70 for a start and the ligand refines fine. <br>
</font></p>
<font face="Arial">I noticed that in the first
macrocycle with and initial factor of 20, the B's are
nearly unchanged (20 +- 2) Red diff density appears as
expected. In the second cycle The minimizer let the
B-factors "explode" to about 200 and that basically is
the overkill and it never recovers.<br>
<br>
HTH<br>
<br>
Cheers<span class="HOEnZb"><font color="#888888"><br>
<br>
Christian<br>
�</font></span></font>
<div>
<div class="h5"><br>
<div class="m_-889494717917611925moz-cite-prefix">Am
31.10.2016 um 15:59 schrieb Dorothee Liebschner:<br>
</div>
<blockquote type="cite">
<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
moz-do-not-send="true"
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="m_-889494717917611925HOEnZb"><font
color="#888888">
<p><font face="Arial"><br>
Christian</font></p>
</font></span>
<div>
<div class="m_-889494717917611925h5">
<p><font face="Arial"><br>
</font></p>
<p><font face="Arial"><br>
</font></p>
<br>
<div
class="m_-889494717917611925m_-3740913058495017715moz-cite-prefix">Am
06.09.2016 um 01:44 schrieb Pavel
Afonine:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="m_-889494717917611925h5">
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_-889494717917611925m_-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
moz-do-not-send="true"
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>
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