[3dem] Changing symmetry from C1 to D2
Jonathan Flores
florejo at ohsu.edu
Tue Sep 28 16:03:35 PDT 2021
Hi Raja—
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.
Be sure to sufficiently lowpass-filter the reference. Otherwise relion may have issues aligning your particles due to asymmetric features in the reference.
The relion_image_handler command you listed is not necessary for your intended application (if i understand your problem correctly)
On Sep 28, 2021, at 1:56 PM, Raja Dey <rddey80 at gmail.com<mailto:rddey80 at gmail.com>> wrote:
Hi,
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:
-------------------------------------
relion_align_symmetry --i InitialModel/job017/run_it150_class001.mrc \
--o InitialModel/job017/run_it150_class001_alignD2.mrc --sym D2
And after confirming in UCSF Chimera or relion_display 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:
relion_image_handler --i InitialModel/job017/run_it150_class001_alignD2.mrc \
--o InitialModel/job017/run_it150_class001_symD2.mrc --sym D2
The output map of the latter command should be similar to the input map. You could check this by:
relion_display --i InitialModel/job017/run_it150_class001_alignD2.mrc &
relion_display --i InitialModel/job017/run_it150_class001_symD2.mrc &
------------------------------------------
and created the map
refjob30_ct25_class001_symD2.mrc Please see below
<image.png>
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).
It didn't work and resulted in a totally useless map.
While the same data sets can produce good map with D2 symmetry in cryosparc.
Can someone help creating a good map in relion with D2 symmetry?
Thanking you in advance...
Best regards,
Raja
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