[3dem] Changing symmetry from C1 to D2

[Raja Dey]

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: 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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