Leginon

Hi Justus,

I had the same problem and what I ended up doing was to just write down the magnification steps on the microscope by turning the mag knob through each step and writing them all down.

Then edit the file c:\Python23\Lib\site-packages\pyScope\tecnai.py

The magtable variable corresponds to the camera magnification and mainscreenmagtable corresponds to the main screen magnification. This takes a little while..

I had the same problem, when I would send a particular preset, the mag was always off by some amount. This fixed the problem. Apparently different polaras have different magtables. If you run into any problems, feel free to contact me sexton@stanford.edu .

Cheers,

Jonny

thanks a lot, the presets are correct now. didn't take (much) more than 5 minutes. :)

j.

I've started to have similar problems to those described at the beginning of the thread - I take a preset from the microscope with a given magnification and then when I send the preset back to the microscope the magnification jumps up a step. The problems started after an FEI engineer completely re-installed the software from scratch on the Tecnai F20's PC. The problems do not appear to happen with magnifications of 29000 and below. The current release of pyScope (1.0.5) on the PC does not have the tables described earlier in the thread in the tecnai.py although there is a similar table in tecnai2.py. Also, based on the drop down list of magnifications that is obtained when attempting to edit the preset, Leginon appears to think there is an extra magnification (40000) that is not currently supported on our microscope (but possibly it was before the Tecnai microscope software was re-installed, possibly in a different release version). Attempting to add a dummy magnification for 40000 in tecnai2.py (on the microscope PC/ Leginon client system) did not help,

William

I tried a different workaround than before. I first created a new instrument for the Tecnai using the dbemtools admin tools and also changing the old instrument for the Tecnai so it no longer had the correct hostname. The latter step ensured that the new instrument (with the correct hostname) was picked up when running Leginon. I found that doing these steps on their own gave errors from Leginon when attempting to send presets to the microscope (i.e. rather than incorrect behaviour with an error message as before). So then in phpMyAdmin (after struggling with MySQL to get the syntax exactly right due to quotation marks or escapes I think) I inserted a new record in the MagnificationsData table for the new instrument with the correct list of magnificaitons in the SEQ|magnifications field. The INSERT that was done was (more or less):

INSERT INTO MagnificationsData (DEF_timestamp, 'SEQ|magnifications', 'REF|InstrumentData|instrument') VALUES (NOW,'[...]', 19);

where "[...]" actually had the new list of magnifications in the square brackets.

I'm still confused why this fix was necessary and maybe there was a better way to do it. Also, something may still be broken (as for example maybe another change was necessary in the database to fix things properly). It seems like either dbemtools and/ or Leginon should be looking after the required steps to make sure the new instrument is handled in the correct way. Anyway, subsequent to the change in the MagnificationsData table in the database and the earlier creation of a new Tecnai instrument it appears that sending presets now works correctly again (although I was unable to test things fully due to other problems with our microscope at present - I sent and received presets in my tests with the column valves closed),

William