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eisfabian / PACEtomo

Parallel cryo electron tomography via beam image shift
GNU General Public License v3.0
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PACEtomo_selectTargets leaving low dose mode when realigning before measure geometry #14

Closed cdienem closed 1 year ago

cdienem commented 1 year ago

Dear Fabian,

I encountered an issue with measuring sample geometry from the Targets window. It first realigns to the tracking item, however, it seems to leave low dose mode, which makes the script hang. It complains that it needs to be in low dose mode to perform subsequent steps. I looked into the script line where the realignment is done:

https://github.com/eisfabian/PACEtomo/blob/68e0e0b5de84b5000cedc570a36f2c5135eb38f9/PACEtomo_selectTargets.py#L398

and saw, that it is set to not restore the state after realigning. I changed 0 -> 1 and it seems to work now. Was there a rationale behind setting the second parameter to 0?

Best, Chris

eisfabian commented 1 year ago

Hi Chris,

Thanks! I did not consider SerialEM leaving low dose during the procedure. Do you collect your maps outside of low dose?

If I remember correctly, the rationale was that it should stay in Record mode after aligning to save some time in case the realign was started from View mode. But I guess it's safer to have it return to the original state first. I will change it accordingly!

Best wishes, Fabian