Configure leginon.cfg¶

For older versions of Appion and Leginon (pre-2.2), please use the following instructions:
Instructions for Appion and Leginon versions prior to 2.2

The order in which Leginon/Appion looks for leginon.cfg¶

1. individual user home directory
2. where leginon python modules are loaded from. In an installed case, $PYTHONSITEPKG/leginon
    
   Note: You can discover the $PYTHONSITEPKG path by starting python:
   

   python
   import sys
   sys.path
   

   
   The first path to site-packages should hold the config file.
    
3. /etc/myami (on Unix)

Locate the search directories and the currently loaded cfg files by running the following python script in $PYTHONSITEPKG/leginon¶

configcheck.py

Configuration file template¶

A skeleton (default) configuration file is available:

/path/to/myami/leginon/leginon.cfg.template

Create a global leginon.cfg¶

Copy leginon.cfg.template to leginon.cfg.

sudo cp -v /path/to/myami/leginon/leginon.cfg.template /etc/myami/leginon.cfg

Edit the newly created file and add a directory for images. Make sure you have permission to save files at this location. See File Server Setup Considerations for more details

You may put in a fake path on the microscope PC installation and ignore the error message at the start of Leginon if you follow our general rule of not saving any image directly from the microscope pc,

[Images]
path: /your_storage_disk_path/leginon

This serves as the global leginon configuration.

Individual User leginon.cfg¶

For individual Leginon users, the above file can be copied to their home directory and the following added once they have registered as a Leginon user. This extra configuration will allow individual user to skip the step of selecting his/her name from the user list.

[User]
fullname: your_firstname your_lastname

• Important: The name should be typed exactly as registered with firstname followed by lastname.
  For example, you entered John as firstname and Doe as lastname during registration, you should enter "John Doe" for fullname, not "Doe, John" nor "john doe"

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