Leginon

h1. Steps involved in the installation

See [[Installation Troubleshooting]] 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/myamiweb/admin.php'

If the login system is activated, you will have to log in as administrator user.

h2.  Add yourself as a User

{{include(Set up for a new regular user shared)}}

h2.  Add your mircoscope as an TEM instrument

*  Click on Instruments.

*  Add a "name" (required and [[More about Instruments#Valid Instrument Names|not arbitrary]]--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 [[More about Instruments#Valid Instrument Names|not arbitrary]]--Gatan cameras are all called "Gatan"/Tietz cameras all have different names). Follow the cases! (a unix requirement)

See the section on [[More about Instruments#Valid Instrument Names|Instrument Tool]] 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.  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.

bq. 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.

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

* !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

[[Add a new project for test|Add a new project for testing installation]]. The rest of this chapter is for references.

[[Recommandation for setup at a new institute|< Recommandation for setup at a new institute]] | [[Add a new project for test|Add a new project for testing installation >]]