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<p>Hi Philippe,</p>
<p>there is no option to exclude atoms from refinement in
phenix.rea_space_refine, but in your case this work-around may
just do the job.. Use reference model restraints for the
misbehaving part of the model. You can do that in two ways: 1) by
restraining to the initial model itself or 2) by providing an
external model for that region. I'm not sure which one would work
best in your case soyou may end up trying both.<br>
</p>
<p>Let me know if you need any help with this and I will help you
set this up (off-list). For this I may need your model and map
files so that I send you back a working example.<br>
</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 5/15/23 07:03, CUNIASSE Philippe
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:4FFA270A-A9BD-4B13-B91A-112CD18BAE9C@cea.fr">
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<p class="MsoNormal"><span style="font-size:12.0pt">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt" lang="EN-US">I
am trying to do a phenix.real_space_refine in a CryoEM map
at 4.2 Å with a model obtained by MDFF (NAMD, a protein DNA
complex) because the resulting structure, despite a good CC
and a good molecular geometry has a poor Ramachandran Map.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt" lang="EN-US">When
doing the phenix.real_space_refine, the CC is slightly
increased with respect to the starting structure, the
Ramachandran is dramatically increased but some part of the
model ( in the case, the first three bases pairs a DNA
duplex) are strongly distorted because of a lack of density
in the corresponding region of the map.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt" lang="EN-US">For
some reason, this does not append with the MDFF method.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt" lang="EN-US">I
was wondering if there is a mean, in
phenix.real_space_refine, to exclude a part of the model
from being fitted in the map. Indeed, the distortion I
observe in the DNA duplex is likely due to the fact that the
real_space_refine tries to put the atoms at the extremity of
the duplex in the closest density at the price of a strong
distortion of the structure.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt" lang="EN-US">Thank
in advance for your suggestions.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt" lang="EN-US">Best
regards.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt" lang="EN-US">Philippe.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></p>
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