Leginon

h1. Test run operation problems

* [[Test_run_operation_problems#Python-and-Leginon-windows-do-not-stay-opened-on-Windows-PC|When Leginon or Leginon Client is launched,Python window opens and closes instantaneously on Windows]]

* [[Test_run_operation_problems#Missing-modules|ImportError "No module named xxxx"]]

* [[Test_run_operation_problems#Tecnai-does-not-show-up-in-instrument-list|Microscope or CCDCamera name does not show up in the

Leginon instrument list in Instrument Node]]

* [[Test_run_operation_problems#Tecnai-does-not-show-up-in-instrument-list|The Microscope computer where Leginon Client runs does

not show up in the Launcher list of Leginon when opening an application]]

* [[Test_run_operation_problems#Magnification-list-not-in-the-database|No Magnification saved for xxx(your

scope)]]

* [[Test_run_operation_problems#Leginon-fails-to-aquire-and-save-larger-images|Leginon fails to collect 4kx4k images]]

h2. 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.

h2. Missing modules

*_Why:_*

*  Either the python path is not set up correctly or the module was not installed

properly.

*_Testing:_*

* script: <link linkend="inst_syscheck">syscheck.py</link>

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.

h2. "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)

* *

Follow instruction in pyScope Bulletin Board Thread  "Testing if pyScope is working with your TEM or CCD":http://emg.nysbc.org/boards/7/topics/607.

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

this:<pre>Python>from pyScope import tecnai

Python>myscope = tecnai.Tecnai()

Python>myscope.getMagnification()</pre>

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

h2. 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.

h2. 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.

h2. 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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[[Administration Tool problems|< Administration Tool problems]] | [[Network problems|Network problems >]]

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