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<span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">Hi Raja—</span>
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<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">If I understand your inquiry correctly, you will want to take the output from your relion_align_symmetry command and use that directly in your subsequent 3D auto-refine job with symmetry
applied. </div>
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><br class="">
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<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">Be sure to sufficiently lowpass-filter the reference. Otherwise relion may have issues aligning your particles due to asymmetric features in the reference.</div>
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<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">The relion_image_handler command you listed is not necessary for your intended application (if i understand your problem correctly)</div>
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<div class="">On Sep 28, 2021, at 1:56 PM, Raja Dey <<a href="mailto:rddey80@gmail.com" class="">rddey80@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Hi,
<div class="">I am having a problem changing the symmetry from C1 to D2. I have a 3D auto-refined map created in C1 where I can see secondary structures and now want to switch to D2. I followed as enclosed below:</div>
<div class=""><span style="font-family: CMTT10; font-size: 10pt; white-space: pre-wrap;" class="">-------------------------------------</span><br class="">
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<pre style="white-space: pre-wrap;" class=""><span style="font-size:10pt;font-family:CMTT10" class="">relion_align_symmetry --i InitialModel/job017/run_it150_class001.mrc \
--o InitialModel/job017/run_it150_class001_alignD2.mrc --sym D2
</span></pre>
<p style="" class=""><span style="font-size:10pt;font-family:CMR10" class="">And after confirming in UCSF Chimera or </span><span style="font-size:10pt;font-family:CMTT10" class="">relion_display </span><span style="font-size:10pt;font-family:CMR10" class="">that
the symmetry axes in the map are now indeed aligned with the X, Y and Z-axes, we can now impose D2 symmetry using:</span></p>
<pre style="white-space: pre-wrap;" class=""><span style="font-size:10pt;font-family:CMTT10" class="">relion_image_handler --i InitialModel/job017/run_it150_class001_alignD2.mrc \
--o InitialModel/job017/run_it150_class001_symD2.mrc --sym D2
</span></pre>
<p style="" class=""><span style="font-size:10pt;font-family:CMR10" class="">The output map of the latter command should be similar to the input map. You could check this by:</span></p>
<pre style="white-space: pre-wrap;" class=""><span style="font-size:10pt;font-family:CMTT10" class="">relion_display --i InitialModel/job017/run_it150_class001_alignD2.mrc &
relion_display --i InitialModel/job017/run_it150_class001_symD2.mrc &</span></pre>
<pre style="white-space: pre-wrap;" class=""><span style="font-size:10pt;font-family:CMTT10" class="">------------------------------------------</span></pre>
<pre style="white-space: pre-wrap;" class=""><span style="font-size:10pt;font-family:CMTT10" class="">and created the map </span></pre>
<pre style="white-space: pre-wrap;" class="">refjob30_ct25_class001_symD2.mrc Please see below</pre>
<pre style="white-space: pre-wrap;" class=""><br class=""></pre>
<pre style="white-space: pre-wrap;" class=""><span id="cid:ii_ku4jw8sx0"><image.png></span><br class=""></pre>
<pre style="white-space: pre-wrap;" class=""><span style="font-size:10pt;font-family:CMTT10" class="">Now used the above map as a reference map in 3D auto-refinement run with the same extracted particles(that were without binning and used in the earlier 3D auto-ref run with C1-sym). </span></pre>
<pre style="white-space: pre-wrap;" class=""><span style="font-size:10pt;font-family:CMTT10" class="">It didn't work and resulted in a totally useless map. </span></pre>
<pre style="white-space: pre-wrap;" class=""><span style="font-size:10pt;font-family:CMTT10" class="">While the same data sets can produce good map with D2 symmetry in cryosparc.</span></pre>
<pre class=""><font face="CMTT10" class=""><span style="font-size:10pt;white-space:pre-wrap" class="">Can someone </span><span style="white-space:pre-wrap;font-size:13.3333px" class="">help </span><span style="font-size:10pt;white-space:pre-wrap" class="">creating a good map in relion with D2 symmetry? </span></font></pre>
<pre class=""><font face="CMTT10" class=""><span style="font-size:10pt;white-space:pre-wrap" class="">Thanking you in advance...</span></font></pre>
<pre class=""><font face="CMTT10" class=""><span style="font-size:10pt;white-space:pre-wrap" class="">Best regards,</span></font></pre>
<pre class=""><font face="CMTT10" class=""><span style="font-size:10pt;white-space:pre-wrap" class="">Raja</span></font></pre>
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