Using Leginon at Scripps » History » Version 13
Amber Herold, 02/23/2011 01:08 PM
| 1 | 1 | Jim Pulokas | h1. Using Leginon at Scripps |
|---|---|---|---|
| 2 | |||
| 3 | 9 | Jim Pulokas | h2. TSRI Login/Email Account |
| 4 | 1 | Jim Pulokas | |
| 5 | 8 | Jim Pulokas | 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. |
| 6 | 1 | Jim Pulokas | |
| 7 | 5 | Jim Pulokas | h2. CIMBio Scheduler |
| 8 | |||
| 9 | 12 | Christopher Irving | You will log in to the CIMBio Scheduler to reserve time on the TEM. Log in at "cimbio.scripps.edu/scheduler":http://cimbio.scripps.edu/scheduler . If don't already have a login please send a request to scheduler@emg.nysbc.org. |
| 10 | 5 | Jim Pulokas | |
| 11 | h2. Tecnai Windows PC Account |
||
| 12 | |||
| 13 | 11 | Christopher Irving | 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. |
| 14 | 5 | Jim Pulokas | |
| 15 | 1 | Jim Pulokas | h2. Myami Account |
| 16 | |||
| 17 | 11 | Christopher Irving | 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 |
| 18 | 1 | Jim Pulokas | |
| 19 | 3 | Jim Pulokas | h2. Running Leginon |
| 20 | |||
| 21 | * Log in to the Windows workstation that is connected to the TEM |
||
| 22 | * Start the Tecnai User Interface (TUI) |
||
| 23 | 1 | Jim Pulokas | * Tecnai 1 only: Start DigitalMicrograph. Insert the camera. (may also have to reinsert it any time you open the column valves) |
| 24 | * Start "Leginon Client" (aka: launcher.py) |
||
| 25 | 5 | Jim Pulokas | * The Leginon Client window will be empty, as it is waiting for a connection from the main Leginon program |
| 26 | 1 | Jim Pulokas | * 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. |
| 27 | 10 | Christopher Irving | * Open a command terminal and enter the following command:<pre>/ami/sw/bin/betaleginon</pre> |
| 28 | 6 | Jim Pulokas | * 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. |
| 29 | 5 | Jim Pulokas | |
| 30 | 6 | Jim Pulokas | h2. Troubleshooting |
| 31 | 5 | Jim Pulokas | |
| 32 | 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. |
||
| 33 | |||
| 34 | h2. Links |
||
| 35 | |||
| 36 | * Leginon User's Guide: http://emg.nysbc.org/projects/leginon/wiki/Leginon_Manual |
||
| 37 | * Bugs and other issues can reported here: http://ami/redmine/projects/leginon/issues. |
||
| 38 | * There is a Leginon forum where people discuss problems/solutions and you may find some hints: http://ami/redmine/projects/leginon/boards |
||
| 39 | 13 | Amber Herold | |
| 40 | [[Visitors Guide Shared]] |