Hi,
I’ve noticed that when spherical aberration, tetrafoil and anisomag are refined in global CTF (at least when run on-the-fly in homogenous refinement), a small non-zero phase shift is refined, for data where the phase shift ought to be zero (collected without a phase shift, and where no phase shift was refined during Patch CTF).
Is this expected, and what is the explanation? Sorry if I am being dim and missing something obvious…
Cheers
Oli
@olibclarke Please can you post the output of the command (replacing P99, J199 with the job’s project and job IDs, respectively):
cryosparcm cli "get_job('P99', 'J199', 'job_type', 'version', 'params_spec')"
Hi Wolfram, here you go (not the same job, but same issue/observation):
{'_id': '687e27b9341f26de60df8d53', 'job_type': 'ctf_refine_global', 'params_spec': {'crg_do_spherical': {'value': True}, 'crg_do_tetrafoil': {'value': True}, 'crg_num_iters': {'value': 2}}, 'project_uid': 'P11', 'uid': 'J371', 'version': 'v4.7.1'}
Dear @olibclarke,
When fitting any of the even order terms in the CTF (spherical aberration, tetrafoil) and anisomag (due to induced updates in defocus), all other even order terms are re-fit, and this includes the “phase shift” which is a constant (0th order) term in the CTF phase.
However, the “phase shift” encapsulates both a phase-plate induced phase shift, as well as a small correction arising straight from the amplitude contrast. This value is default set to 10% in Patch CTF, a small value, but from my understanding the typical recommendation value of between 7-10% is imprecise and can actually vary. So in effect, re-estimating the phase shift really is more of a correction on the amplitude contrast.
(The phase shift is the w term in Singer and Sigworth, 2020. Eqn 8 shows a simplified CTF model omitting astigmatism, 3rd order terms, and tetrafoil)
Best,
Michael
Thank you Michael - I figured it might be a fudge factor for AC, but couldn’t find it explicitly stated anywhere in the docs/guide that this was refined in the general CTF model in CS, so this is helpful to know.
Out of curiosity, did the grid have a carbon film support?
It did as a matter of fact! Thin carbon
