ASYM card, defocus refinement
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I am reading your Frealign paper. I got several questions:
1) The parameter ASYM could be I, I1, I2, what is the difference? Is it related to the input initial model?
2) In 4.4. "Particle parameters" of your paper, there are two sentences as (in quotes):
"The refinement of these parameters is done for entire groups of particles from single micrographs to boost the signal and accuracy of the refinement. However, if data are included in the refinement at a resolution higher than 10 Å, as specified by the control parameter RMAX2, the refinement of CTF parameters is done individually for each particle."
So according to the above, if you turn on defocus (T) or astigmatism refinement (T), would it be correcting for each particle automatically? What is the requirement for defocus and/or astigmatism refinements?
I, I1 and I2 are all for
I, I1 and I2 are all for structures with icosahedral symmetry. I and I1 use the same conventions for the three symmetry operators. I2 uses another convention (see definitions in the program code). You should try both and see which one will produce the convention you are using.
For CTF refinement, you should not refine the defocus for individual particles as there is hardly ever enough signal. But if you want to try, Frealign will switch from defocus refinement per micrograph to defocus refinement per particle if you set FPART to 'T'.
You should use CTF values that you obtain from CTFFIND or CTFTILT and not refine them until you have reached the highest possible resolution with the refinement of the other parameters.
The CTF correction is always done per particle, independently of how you refine it.