Leginon

h1. Gatan on Windows with SEMCCD.dll

dmsem module uses SEMCCD.dll written for SerialEM to communicate with Gatan software rather than tecnaiccd.dll

If using this on a computer different from the scope computer, please read [[Using_Leginon_on_a_system_where_the_microscope_and_camera_are_controlled_by_different_computers|this]] first.

h2. Extra Package and Installation

* Use all win32 version of Windows installer if this is an Windows-32 PC.  Otherwise install the 64-bit version.

* SerialEM DigitalMicrograph Plug-in

{{include(Install_SerialEM_DigitalMicrograph_plugin)}}

h2. instruments.cfg

Currently UltraScan and Orius camera are supported.

For UltraScan camera (US4000), set instruments.cfg to use GatanUltraScan class. For example:

<pre>

[us4000]

class: dmsem.GatanUltraScan

zplane: 50

height: 4096

width: 4096

</pre>

For Orius camera, set instruments.cfg to use GatanOrius class.

h2. Setup

{{include(dm camera configuration)}}

h2. Define local configuration in dmsem.cfg

# Copy from your myami checkout pyscope/dmsem.cfg.template to C:\Program Files\myami\dmsem.cfg

# Make changes to the configured value in dmsem.cfg

Most parameters are explained above.

* *The config parser takes "'" and "\" literally*.  Therefore, do not include "'" in DM_VERION.  In addition, the path separator should be "\"

* *CAMERA_ID* is usually 0 if it is the only Gatan camera.

* *Ultrascan camera should be configured under utrascan module, and Orius camera should be configured under orius module.

For example, only UltraScan camera exists on this computer that has Digital Micrograph version 2.32.788.0, and DM camera configuration

has vertical flip but no rotation, then set the dmsem.cfg ultrascan module like this:

<pre>

[dm]

DM_VERSION = 2.32.788.0

[ultrascan]

CAMERA_ID = 0

FLIP = True

ROTATE = 0

</pre>

h2. Testing with pyscope

{{include(Gatan_UltraScan_dmsem_Installation_Pyscope_Test)}}

h2. Trouble shooting

h3. Refused socket connection

{{include(trouble shooting semccd socket connection)}}

h3. SerialEM-CCD plugin can output the command it issues and results to DM's result panel if you set the environment variable SERIALEMCCD_DEBUG to larger than 0.  Set to 1 to show general log. Set to 2 to also include socket communication log.  Please activate this debug log and include the portion that shows problem when reporting problems to Leginon team.

h2. Programs to open before Leginon Client: Digital Micrograph