Leginon

Check this page Check_Cs_value_match_before_using_Leginon_after_update Make sure you have followed it. If you didn't, send me mysql dump of leginondb table InstrumentData so that I can assess the damage and find ways to repair it.

You will also find similar case in later part of this posting http://emg.nysbc.org/boards/6/topics/1259

Anchi

I looked over the InstrumentData table you sent. There is something strange. The name column in InstrumentData is the class attribute "name". We did not make a class with "name" attribute "TecnaiF30". That particular row of data must be your original instrument before the update since it does have the Cs value, but you must have changed the "name" field. When Leginon started after the upgrade, it could not find the row of data that matched the "host" tecnai-f30 and "name" Tecnai, so it tried to insert a new one.

In addition, it looks like you failed to include Cs value in your instrument.cfg see How_to_Update_from_v21_(Microscope_Windows_Computer) to include Cs value. Therefore the new insert has no cs value.

Here is what you need to do:

1. Make sure you get the instrument.cfg correct.

On the microscope computer, this should be (from what you put in the database during schema update) assuming you still have the tietz under it,

[tem]
class: tecnai.Tecnai
cs: 2.26e-3
[tietzcam]
class: tietz.TietzSCX
zplane: 5

On gatan's computer for k2, follow this Gatan_K2_Installation_Notes

2. Repair your InstrumentData table.

• change "Tecnai" to something else, like "wrongTecnai" in the "name" field on row with DEF_id=18. I don't want to delete it in case you've already saved an image with that. If you didn't get that far, you can simply delete the row of data.
• change the data row DEF_id=9 back to name="Tecnai", not "TecnaiF30"

3. When you start Leginon, you should get three new rows of data for the three modes of K2 with the name field of "GatanK2Linear","GatanK2Counting","GatanK2Super" on the same host gatan-k2 but nothing else.

Post your exact instrument.cfg here if you still have problem.

Anchi

I edited the InstrumentData table:

1. Removed the row of DEF_id=18

2. Changed "name" attribute of 'tecnai-f30' to 'Tecnai'

3. Changed "name" attribute of 'Gatan-k2' to 'gatank2' (DEF_id=17)

We started a new Legion session, no longer had the same preset errors, and could see the three instruments listed when we ran an application.

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When I ran cscheck.py on the main server, the returne is still

TEM tecnai-f30.Tecnai used in session 12may16a has Cs value of 2.260e-03 m

Perhaps it is retrieving an earlier session record but not the most recent one?
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Thank you

Harry

About the result of cscheck.py It is odd that it didn't find the most recent session. The reverse sort timestamp of the SessionData creation. Well, as long as it works, it is fine.

Anchi