Global CTF refinement

CTF Refinement
#1

Hi,
I have a couple of sessions where groupID was not defined when the micrographs were imported into the session. Consequently, I am writing scripts to set groupID for particles, according to their originating micrographs, in mid session. If I perform Global CTF refinement with options Fit Tilt and Fit Trefoil, are ctf/shif_A, ctf/tilt_A, and ctf/trefoil_A the only cs (file) fields that are updated?

Here is a section from the output

[CPU: 2.30 GB] Previous group params:
[CPU: 2.30 GB] Shift (A): [0. 0.]
[CPU: 2.30 GB] Tilt (A): [0. 0.]
[CPU: 2.30 GB] Tilt (mrad): [0. 0.]
[CPU: 2.30 GB] Trefoil (A): [0. 0.]
[CPU: 2.30 GB] New group params:
[CPU: 2.30 GB] Shift (A): [0.09158283 0.09160191]
[CPU: 2.30 GB] Tilt (A): [ 9452.94957951 12304.3968832 ]
[CPU: 2.30 GB] Tilt (mrad): [0.35010924 0.4557184 ]
[CPU: 2.30 GB] Trefoil (A): [3119.76531163 -319.86023387]
[CPU: 2.30 GB] Updating tilt values for group.
[CPU: 2.30 GB] Updating trefoil values for group.
[CPU: 2.30 GB] ------- Group 2 -------

#2

Did you consider comparing the values inside the relevant columns of the cs files in question? There is a tutorial explaining the cs file format and providing motivating examples.

#3

Hi,
Yes there is a tutorial and I have written the scripts to make the changes. However, the tutorial does not indicate which fields are modified during group CTF refinement. I was concerned that my script does not extract information from all fields that are updated during CTF group refinement. Are the above mentioned fields the only fields that are updated?

#4

Hi @rkhayat,

Currently, the cs files don’t store information about which fields have been modified within a result group, so in general one can only tell whether the groups as a whole are modified (i.e. CTF refinement will modify ctf but not alignments3D for example). Wolfram’s suggestion of comparing columns of the cs file before and after a job is, in general, the only way one would determine which exact fields are modified within a result group.

For CTF Refinement in particular though, you are correct in stating that ctf/shift_A, ctf/tilt_A and ctf/trefoil_A are the only CTF parameters modified if the “Fit tilt” and “Fit trefoil” options are activated.

Best,
Michael

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