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Test run operation problems

Python and Leginon windows do not stay opened on Windows PC

Why:

  • Windows closes the python process window because an error is detected.

Testing: Start Leginon from a python command window so that the error message can be read

  • Follow the following menu to open a python command window:

Windows/Start Menu/All Programs/Python2.5/Python (command line)

  • Python> import start

  • Read the error message. Copy it to your bug report when asking NRAMM for help.

Missing modules

Why:

  • Either the python path is not set up correctly or the module was not installed properly.

Testing:

  • script: syscheck.py

If the missing module is not installed under one of the Python module search path found in the syscheck output, it need to be moved.

"Tecnai" does not show up in instrument list

Why:

  • An error is detected when the instrument is loaded.

_Testing: Import the module in pyScope package through a python command window so that the error message can be read_

  • Follow the following menu to open a python command window:

Windows/Start Menu/All Programs/Python2.5/Python (command line)

For example, if "Tecnai" is missing from the instrument list, try

Python>from pyscope import registry
Python>registry.getClasses()
Python> myscope = registry.getClass('Tecnai')()
Python> myscope.getMagnification()

  • The "registry.getClasses() command will show you in tuples, the class name, followed by the class object. Use the class name as the input for getClass command.

  • Read the error message. Copy it to your bug report when asking for help.

Magnification list not in the database

Why: first time the TEM is used by leginon and the database, the valid magnification for the instrument needs to be saved in the database.

Solution: On the scope: Leginon/Instrument> select the microscope to display parameters and click "Get Magnification" button (The icon is of a calculator) on the tool bar.

Leginon fails to aquire and save larger images

Why:

  • Your computer does not have sufficient memory to acquire and correct the large 4kx4k images.

Solution:

Put on your computer more memory and more memory swap space.

  • If you file storage system is not on the same computer, there may be problem transfering large data file. This is known to happen from a Windows machine to disk storage operated under Linux through Samba.

Solution:

Let us know if you have one.

Leginon fails to move the goniometer after a new installation or update of pyScope

Why:

  • tecnaicom.py, the python wrapper of Tecnai Scripting library, has not been created in the running pyScope folder on the microscope controlling computer.

Solution:

Double click updatecom.py to run it in the (installed) pyScope folder.

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