Leginon

The missing calibration is the beam tilt defocus calibration for the preset you used for the focusing step. Did you change your fa preset magnification from what you or others in your group might have used before? You will need to calibrate for your required mag.

I noticed that the MSI-tomography manual uses F30 examples for presets not F20 which were used in other MSI manual. Did it cause confusion that made you realize that you were using an magnification that has not been calibrated? I can add the F20 set if this was indeed the case to make the manual easier to follow.

Anchi

no, problem was not knowing from the error message which matrix was not calibrated, but then, it occurred in the focus node so maybe I should have inferred.
Thanks for the quick turnaround!
Cheri

I repeated beam tilt defocus calibration for the preset and still get the same error.

Could you post screen shot of your focus step settings (Leginon/Tomography_Focus/Focus_Sequence dialog with "Fine_Tilt" highlighted) and PresetManager node with the preset you used in that focus step so that we are sure that they match?

You can also use the measure tool in Beam_Tilt node to test by sending the preset indicated in your focus step to scope and then try to measure defocus there.

"missing calibration matrix" is only printed during beam-tilt based operation.....

Also, if you just want to try tomography, you can deactivate this particular focus step. If your goniometer behaves well (smooth movement and more and less symmetrical), the stage_tilt focusing steps before the Fine_tilt step should get you close enough to try out.

also, failure to fit focus error

here are snaps for focus steps and presets

But the fit focus warning is a different one and it is only a warning. It can only appear if you have gotten past the first error you reported about missing calibration! Therefore, I have to assume that the original error is gone, meaning that you don't get new one that appears in the log. The indicator by the node selector shows the most recent status so you may see the old one if no new one overtake it.

Now the problem is a common focusing problem not a calibration one.

I added a section on Optimizing_Autofocus in the manual that may help you solve that. From what I can tell, because you choose to use 29000x for fa preset, the fit limit will need to be adjusted.