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[SOLVED] Error messages while attempting to calibrate microscope with current myami-beta

Added by Patrick Goetz over 5 years ago

Hi -

We're testing out myami-beta and have run into some issues calibrating the microscope. In particular, we're getting this error message:

Welcome to DigitalMicrograph.  2/19/2019, 10:12:13 AM
SerialEMSocket: Function code not found: 47.
  MOST LIKELY THIS PLUGIN NEEDS TO BE UPGRADED TO MATCH THE SERIALEM VERSION
SerialEMSocket: Function code not found: 47.
  MOST LIKELY THIS PLUGIN NEEDS TO BE UPGRADED TO MATCH THE SERIALEM VERSION

This was all working with the previous stable version of myami. Any thoughts on where to look for a solution?


Replies (8)

RE: Error messages while attempting to calibrate microscope with current myami-beta - Added by Anchi Cheng over 5 years ago

Going to need some more details. Which calibration were you doing when this show up ? Is this on K3 with energy filter or other cases. The only recent (half-a-year) change is a call to get energy offset of the energy filter. It is not yet called by anything in leginon, so you should not have encounter it. I will also need to use the version of SEMCCD plugin. A date of the file is usually an indication of its version if it is not spelled out.

RE: Error messages while attempting to calibrate microscope with current myami-beta - Added by Patrick Goetz over 5 years ago

Thanks, Anchi. I'm headed over to the lab in a few minutes and will try and get more information then.

RE: [SOLVED} Error messages while attempting to calibrate microscope with current myami-beta - Added by Patrick Goetz over 5 years ago

This issue is solved. We needed to set the magnification table on the microscope PC. After we did this, everything started working.

RE: [SOLVED] Error messages while attempting to calibrate microscope with current myami-beta - Added by Anchi Cheng over 5 years ago

Interesting. I did not realize that missing that step would cause this error. Thanks for reporting the solution

RE: [SOLVED] Error messages while attempting to calibrate microscope with current myami-beta - Added by Anchi Cheng over 5 years ago

Did you start a new database ? The old database should have the magnification table. It should also maintain the calibrations. Updating Leginon should not require restarting a database.

RE: [SOLVED] Error messages while attempting to calibrate microscope with current myami-beta - Added by Patrick Goetz over 5 years ago

Yes, it's a complete re-install from scratch using the current myami-beta. Since the database changed from mysql to mariadb, I didn't want to introduce any additional complications.

RE: [SOLVED] Error messages while attempting to calibrate microscope with current myami-beta - Added by Anchi Cheng over 5 years ago

I have some tools for migrating calibrations and presets that will make it smoother next time you attempt this. Once I document it, I will create a link here so that it is easier for you and others next time.

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