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Hi Mark,<br>
<br>
Tom copied me your email.<br>
<br>
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As I'm sure you are aware there is tremendous interest in building
into and refining against low resolution (by X-ray standards) EM
maps. Could you comment to the phenix BB about whether its
appropriate to convert maps to reciprocal space and use ML
refinement?<br>
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<br>
While it is a possible way of doing this (and this is how it's been
done in the past) I don't think it is a good route to follow. In
case of cryo-EM your data is map, so why not just refine against the
map? Why take a detour through reciprocal-space by converting map
into structure factors (=manipulating your original data) and doing
reciprocal space using refinement programs that were designed for
crystallography?<br>
With this in mind we have developed a new refinement tool in Phenix
(it is still in active development!) called phenix.real_space_refine
that is designed to refine atomic models directly into maps (any
map: X-ray, neutron, cryo-EM, low or high resolution), for quick
summary see<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/presentations/real_space_refine.pdf">http://phenix-online.org/presentations/real_space_refine.pdf</a><br>
<br>
as well as documentation page (at the bottom):<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/">http://phenix-online.org/documentation/</a><br>
<br>
and newsletter article (page 43):<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/newsletter/CCN_2013_07.pdf">http://phenix-online.org/newsletter/CCN_2013_07.pdf</a><br>
<br>
Let me know if you have any questions or comments!<br>
<br>
Pavel<br>
<br>
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