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Hi Smith,<br>
<br>
if you've got cryo-EM map, built an initial model into it and want
to refine it then the most natural way to do so is to refine the
model against the map directly and NOT take a detour through
reciprocal space by converting the map into structure factors and
then using the crystallography-specific refinement programs.<br>
<br>
There is a Phenix refinement tool specifically designed for this -
refinement of atomic models into cryo-EM maps or low-resolution
X-ray maps, described here:<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.dropbox.com/s/imv2yzwodik13in/afonine_etal_wcpcw2015.pdf?dl=0">https://www.dropbox.com/s/imv2yzwodik13in/afonine_etal_wcpcw2015.pdf?dl=0</a><br>
<br>
If for whatever reason you still want to do it the old way, then
here are two steps:<br>
- convert the map into structure factors:<br>
phenix.map_to_structure_factors map.ccp4<br>
<br>
- then run phenix.refine the usual way.<br>
<br>
More info at the bottom of this page:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/">http://phenix-online.org/documentation/</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/4/15 6:38 AM, Smith Liu wrote:<br>
</div>
<blockquote
cite="mid:349ca545.15e09.14c84a74af8.Coremail.smith_liu123@163.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div>Dear All,</div>
<div>�</div>
<div>Recently there are cryo-electronic microscopy papers which
refine the reciprocal space of the electronic mcroscopy�map by
phenix refine. For the electronic mcroscopy map, what does it
mean for the reciprocal space? How to get the reciprocal space
map from the� electronic mcroscopy map? In order to realize
this kind of refine in phenx, we only process the xyz
coordinates strategy refine in the graphical interface, right?</div>
<div>�</div>
<div>I am looking forward to getting your reply.</div>
<div>�</div>
<div>Smith</div>
</div>
<br>
<br>
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