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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>
</blockquote>
</div>
</div>
</blockquote>
<br>
<br>
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