Leginon

[[Steps involved in the installation shared]]

h1. Steps involved in the installation

See <link linkend="Inst_Adm">Installation Troubleshooting</link> and  "Leginon Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=2  searching for "admin" if you run into problems.

h2. Go to administration page

Open a web browser. Go to http://yourhost/dbem/admin.php

h2. Add a Group

Groups are used to associate users together. At the moment, Leginon does not use the group association for anything.

*  At http://yourhost/dbem/admin.php, click on Groups.

*  Add a "name" (required) for the group.

*  Optionally enter a full name for the group.

*  Click Save.

h2.  Add Adminstrator User

*  At http://yourhost/dbem/admin.php, click on Users.

*  Add "administrator" as the user.

*  Enter a full name as "administrator". This name should be typed exactly as it is (case-sensitive).

*  Add this user to a previously created group.

*  Click Save.

h2.  Add your mircoscope as an TEM instrument

*  Click on Instruments.

*  Add a "name" (required and <link linkend="instrument_names">not arbitrary</link>--FEI tecnai/polara/spirit series are all called "Tecnai") for the microscope. Follow the cases! (a unix requirement)

*  Enter the hostname of the microscope. Do not captalize the characters!!! (a Window's requirement)

*  Select instrument type TEM.

*  Click Save.

h2.  Add your CCD camera as an CCDCamera instrument

*  Click on Instruments.

*  Add a "name" for the camera (required and <link linkend="instrument_names">not arbitrary</link>--Gatan cameras are all called "Gatan"/Tietz cameras all have different names). Follow the cases! (a unix requirement)

See the section on <link linkend="instrument_names">Instrument Tool</link> for more details.

*  Enter the hostname of the microscope. Do not captalize the characters!!! (a Window's requirement)

*  Select instrument type CCDCamera.

*  Click Save.

h2.  Load the default settings of Legion nodes

*  Click on Default Settings.

*  Click on Load.

h2.  Import Applications

*  Click on Applications.

!http://emg.nysbc.org/software/leginon/images/images/application_on.png!

* Enter the name of the Leginon application XML file. These are files in a subdirectory of your leginon installation called "applications" starting from Leginon v1.3.

<blockquote>

The most commonly used Leginon applications are included as part of the Leginon download. These XML files are in subdirectory of your Leginon download and installation called "applications". The XML files should be imported either using the web based application import tool. Each application includes "(1.5)" in its name to indicate that it will work with this new version of Leginon. The applications that carry the older version name are compatible with the older Leginon.

To find Leginon installation path on Linux:<pre> >start-leginon.py -v</pre>

On Windows, You should find a shortcut to your Leginon installation folder in the "Start Menu/All Programs/Leginon". If not, it is likely

<pre>C:\Python25\Lib\site-packages\Leginon\</pre>

</blockquote>

* !http://emg.nysbc.org/software/leginon/images/images/admin_apptable.png!

*  Select the name of the "To" Host the application will be imported to.

*  Click Import.

h2.  Proceed to First Leginon Test Run Chapter

<link linkend="runleg_chapter">Leginon test runs</link> test for tem/ccd controls and network communications. The rest of this chapter is for references.