Leginon

h1. Getting Started

h2. 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).

h2. Download Leginon System

"http://www.leginon.org/":http://www.leginon.org/

h2. Install Leginon System

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

h2. 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>.

h2. Test run

Refer to <link linkend="runleg_chapter">Start Leginon</link> chapter for test run on

the microscope and on a remote computer.

h2. Align the microscope

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

h2. Calibrate Leginon for the microscope

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

h2. 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>

h2. 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":http://emg.nysbc.org/bb/viewforum.php?f=2 .

h2. 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>

h2. 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 .

h2. Download Leginon System

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

Direct links to downloads:

*  "http://emg.nysbc.org/software/leginon/":http://emg.nysbc.org/software/leginon/

*  "http://emg.nysbc.org/software/dbemtools/":http://emg.nysbc.org/software/dbemtools/

*  "http://emg.nysbc.org/software/mrctools":http://emg.nysbc.org/software/mrctools .

h2. Install Leginon System

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

h2. Add Users, Groups, Instruments, Calibrations, and Applications

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

h2. Test run

Refer to <link linkend="runleg_chapter">Start Leginon</link> chapter for test run on

the microscope and on a remote computer.

h2. 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).

h2. Align the microscope

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

h2. Recording images with Low Dose Kit on the microscope

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

h2. 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>

h2. Help yourself and others

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