Getting Started¶

Full (Super User) Manual - Getting Started¶

These steps are a general overview of walking through the entire procedure involving
installation, microscope alignment, calibrations, and using Leginon applications (e.g.
Manual, Calibrations, MSI).

Download Leginon System¶

http://www.leginon.org/

Install Leginon System¶

Refer to the <link linkend="completeinstall">Complete Installation</link>

Add Users, Groups, Instruments, Calibrations, and Applications¶

Refer to <link linkend="addusers">Administration</link>

For advanced Leginon users who would like to create an application, see the <link
linkend="createapp">application creation chapter</link>.

Test run¶

Refer to <link linkend="runleg_chapter">Start Leginon</link> chapter for test run on
the microscope and on a remote computer.

Align the microscope¶

Refer to <link linkend="microscope_setup">Microscope Set-up</link>

Calibrate Leginon for the microscope¶

Refer to the <link linkend="calapp_chapter">Calibrations chapter</link>

Set-up and Run MSI¶

Refer to <link linkend="MISQuickStart">MSI quick set-up checklist</link>

AND

Refer to <link linkend="leg1operation">MSI Operation</link>

Help yourself and others¶

Refer to <link linkend="Inst_troubleshooting">Installation Trouble Shooting</link>,
<link linkend="MSI_troubleshooting">User Trouble Shooting</link> and Leginon Bulletin Board .

Know the details¶

For advanced Leginon users who would like to create an application, see the <link
linkend="createapp">application creation chapter</link>.

Refer to <link linkend="Nodes">Node Description</link>

Installation (System Administrator) - Getting Started¶

These steps are geared soley towards the system administator(s) that will installing
Leginon and setting it up initially for the rest of the Leginon users that need not be
concerned with these details.

Refer to <link linkend="Inst_troubleshooting">Installation Trouble Shooting</link>, and
Leginon "Bulletin
Board":http://emg.nysbc.org/bb/viewforum.php?f=2 .

Download Leginon System¶

Leginon Home: http://www.leginon.org/

Direct links to downloads:

• http://emg.nysbc.org/software/leginon/

• http://emg.nysbc.org/software/dbemtools/

• http://emg.nysbc.org/software/mrctools .

Install Leginon System¶

Refer to the <link linkend="completeinstall">Complete Installation</link>

Add Users, Groups, Instruments, Calibrations, and Applications¶

Refer to <link linkend="addusers">Administration</link>

Test run¶

Refer to <link linkend="runleg_chapter">Start Leginon</link> chapter for test run on
the microscope and on a remote computer.

Short Manual (Basic Leginon User) - Getting Started¶

These steps are intended to help the basic Leginon user who will operate Leginon (and
not care about installation or the first-time calibrations).

Align the microscope¶

Refer to <link linkend="microscope_setup">Microscope Set-up</link>

Recording images with Low Dose Kit on the microscope¶

Refer to using the <link linkend="manual_app">Manual</link> application

Set-up and run MSI¶

Refer to <link linkend="MISQuickStart">MSI quick set-up checklist</link>

AND

Refer to <link linkend="leg1operation">MSI Operation</link>

Help yourself and others¶

Refer to <link linkend="MSI_troubleshooting">User Trouble Shooting</link>