I’m currently refining a particle in Cryosparc2, with the most up to date version, 2.15.0 I believe. The particle is a viral particle with I4 symmetry, order 120 (rather than order 60 like I symmetry). I’ve seen forum posts saying that Cryosparc2 supports refining in I4 symmetry, however I have yet to see this as a possibility. Attempting refinement with I4 symmetry errors out each time saying that symmetry type is not supported, and a manual inspection of the files shows no I4 symmetry, only I, I1 (identical to I) and I2, all of which have returned subpar refinement results. Any help on how to properly refine an icosahedral particle would be greatly appreciated.
Thanks for this request. We’re actually not too familiar with the definition of I4 symmetry – would you be able to point us toward a resource that defines I4 symmetry as an order 120 symmetry group (instead of 60)?
I’ll preface my response with that I think I confused my symmetry types. The data I’m working on is of the Chikungunya virus, and the order is actually 80 instead of 60 or 120. I had been informed it was I4 symmetry with order 120 when really it was I with T=4 symmetry with order 80.
That said, the spike arrangement still didn’t appear correct when I refined using I or I2 symmetry. I looked into the symmetry code (symmetry.py within the cryosparc_compute directory), and found a reference to an old webpage (the old page for XIMPP) and tracking down their github I found this page https://github.com/I2PC/xmipp-portal/wiki/Symmetry# which is all of their symmetry types, and was able to implement I4, although it wasn’t correct.
I am currently working in cisTEM, which for whatever reason has refined the particle as expected, order 80, using I symmetry.
Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/refine/newrun.py”, line 231, in cryosparc_compute.jobs.refine.newrun.run_homo_refine
File “/data/cryosparc/cryosparc_worker/cryosparc_compute/util/init.py”, line 71, in call
return self[args]
File “/data/cryosparc/cryosparc_worker/cryosparc_compute/util/init.py”, line 73, in missing
ret = self.f(*key)
File “/data/cryosparc/cryosparc_worker/cryosparc_compute/symmetry.py”, line 75, in get_symmetryop
assert False, ‘Missing symmetry file or unrecognized symmetry type: {0}’.format(symstr)
AssertionError: Missing symmetry file or unrecognized symmetry type: I4