[3dem] Changing symmetry from C1 to D2

[Jonathan Flores]

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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