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Hello,<br>
<br>
<blockquote cite="mid:2DF66B89-FF18-421F-AF69-B5755A28C675@riken.jp"
type="cite">
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charset=windows-1252">
<div class="">I am a relative newcomer to Phenix. I have a large
multimeric protein structure docked into an electron density
map, and I would like to further refine it by rigid-body
refinement using Phenix. Is this a realistic strategy?</div>
</blockquote>
<br>
yes, this is a perfectly valid intent. Have a look at <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>
that overviews and summarizes Phenix refinement tools for cryo-EM.<br>
<br>
<blockquote cite="mid:2DF66B89-FF18-421F-AF69-B5755A28C675@riken.jp"
type="cite">
<div class="">I have made some attempts, first by converting the
.mrc map file to .mtz as outlined here:</div>
<div class=""><a moz-do-not-send="true"
href="https://www.phenix-online.org/documentation/reference/map_to_structure_factors.html"
class="">https://www.phenix-online.org/documentation/reference/map_to_structure_factors.html</a></div>
</blockquote>
<br>
If you follow the above link you will see that it is best to refine
the model directly against the map (in real space, that is), instead
of taking a "detour" through reciprocal space.<br>
<br>
So my suggestion to you is:<br>
<br>
- get latest Phenix from nightly builds (it is essential that you
use recent Phenix):<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/download/nightly_builds.cgi">http://phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
- run phenix.real_space_refine (sorry, no GUI yet!):<br>
<br>
phenix.real_space_refine model.pdb map.ccp4<br>
<br>
If you expect the model to make large movements to fit the map, you
can enable morphing or/and rigid-body, and also increase number of
refinement cycles:<br>
<br>
phenix.real_space_refine model.pdb map.ccp4 run=minimization_global+rigid_body+morphing
macro_cycles=10<br>
<br>
<blockquote cite="mid:2DF66B89-FF18-421F-AF69-B5755A28C675@riken.jp"
type="cite">
<div class="">Then I tried to refine using rigid body refinement
in Phenix. However, the program quits but doesn�t really tell me
why. Here�s the last part of the log file:</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">Number of unique models: 24</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� Time building chain proxies: 36.85, per 1000 atoms:
0.26</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� Number of scatterers: 142296</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� At special positions: 0</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� Unit cell: (342, 342, 342, 90, 90, 90)</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� Space group: P 1 (No. 1)</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� Number of sites at special positions: 0</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� Number of scattering types: 4</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� � Type Number� � sf(0)</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">�� � S � � 264 � � 16.00</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">�� � O � 27720� � � 8.00</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">�� � N � 25872� � � 7.00</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">�� � C � 88440� � � 6.00</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">� � sf(0) = scattering factor at diffraction angle 0.</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;
min-height: 13px;" class=""><br class="">
</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">Writing MTZ file:</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">�
/Users/xxx/Documents/Phenix/TEST/Refine_1/Test_refine_data.mtz</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;
min-height: 13px;" class=""><br class="">
</div>
<div style="margin: 0px; font-size: 11px; font-family: Courier;"
class="">Sorry</div>
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Can anyone give me any ideas as to what went wrong?
</div>
</blockquote>
<br>
Still, I would like to debug this.. Could you please send me the
following files:<br>
<br>
- original map;<br>
- MTZ file that you get as result of conversion of this map into
structure factors and the command you use to do this;<br>
- input PDB file with the model;<br>
- phenix.refine command (or GUI setup: .eff file and .log file) that
crashes with the above error message.<br>
<br>
All files will handled confidentially. Files may be large, so please
use Dropbox or any similar file sharing utilities.<br>
<br>
<blockquote cite="mid:2DF66B89-FF18-421F-AF69-B5755A28C675@riken.jp"
type="cite">
<div class="">Also, is there a better way to do this?</div>
</blockquote>
<br>
Yes, see suggestions above!<br>
<br>
Please let me know if you have any questions or need any help!<br>
<br>
Pavel<br>
<br>
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