Using Leginon at Scripps¶

TSRI Login/Email Account¶

You will need a Scripps user name, password, and home directory. This will allow you to log in to our workstations where you will run Leginon. This is normally set up by contacting your group's system administator or TSRI IT Services.

CIMBio Scheduler¶

You will log in to the CIMBio Scheduler to reserve time on the TEM. Log in at cimbio.scripps.edu/scheduler . If don't already have a login please send a request to scheduler@emg.nysbc.org.

Tecnai Windows PC Account¶

You will need to be able to log in to the Windows PC connected to the TEM. Each group has their own account which is shared by the members of that group. If your group needs a login come see Christopher Irving in room CB 112.

Myami Account¶

Running Leginon and accessing the Appion and Leginon Web Tools (myamiweb) will require a new login and password. You will register this the first time you go to the web site: cronus3.scripps.edu/myamiweb

Running Leginon¶

• Log in to the Windows workstation that is connected to the TEM
• Start the Tecnai User Interface (TUI)
• Tecnai 1 only: Start DigitalMicrograph. Insert the camera. (may also have to reinsert it any time you open the column valves)
• Start "Leginon Client" (aka: launcher.py)
• The Leginon Client window will be empty, as it is waiting for a connection from the main Leginon program
• Now log in on the linux workstation where you would like to run the main Leginon program. This will likely be either the one in the TEM room or one in the Control Room.
• Open a command terminal and enter the following command:

  /ami/sw/bin/betaleginon

• This will launch the setup wizard where you will enter your information and create a new session. You will also select the Tecnai PC that you are connecting to.

Troubleshooting¶

If you believe you have found a bug in Leginon, try to find someone in the AMI group to help you. There may be a known solution to your problem. If all else fails, you can revert to using "leginon" instead of "betaleginon". This starts up an older stable version of Leginon, but may be missing some of the latest features.

Links¶

• Leginon User's Guide: http://emg.nysbc.org/projects/leginon/wiki/Leginon_Manual
• Bugs and other issues can reported here: http://ami/redmine/projects/leginon/issues.
• There is a Leginon forum where people discuss problems/solutions and you may find some hints: http://ami/redmine/projects/leginon/boards