Command-Line Mode

In addition to the integrated GUI environment, PARTICLE provides a command-line execution mode (a.k.a. CMX-mode) for "number-crunching" computation in particle screening, alignment, classification and model reconstruction.  The program uses "command definition" files (extension "cmx") created from the GUI to setup the associated parameters for a CMX-mode operation.  After a CMX-mode calculation has been completed, the result can be imported back to the GUI-mode for further processing.  In the following, the CMX functions will be exemplified in a model refinement using the particle stack "myStack.mrc".

Create a CMX Definition

To create a model refinement CMX definition for the particle stack "myStack.mrc" set up the files and parameters in the same way as a GUI operation (namely, loading a reference density map and defining refinement parameters).  Then, export the definition from the Save button (icon) above the CP::3D Model::Reconstruction::Reconstruction Parameter group.  The CMX file will be written to the directory "modeling/" under the default name "myStack.cmx".  To start the model refinement at the command line, go to the "modeling/" directory in the project space, and type at the prompt

$ particle -x myStack.cmx >& run.log &

where the log file is optional, but is very useful for monitoring the progress and debugging.

PARTICLE can run in CMX-Mode for computational intensive tasks such as particle screening, particle alignment, particle classification and model reconstruction.  The respective CMX import/export functions can be accessed from the Save and Load button (icons) located at the top of the following groups:

• Particle screening: CP::Particle::Single Image::Particle Parameter
• Particle alignment: CP::3D Model::Alignment::Particle Alignment
• Particle classification: CP::3D Model::Classification::Classification Parameter
• Model reconstruction: CP::3D Model::Reconstruction::Reconstruction Parameter

Import CMX Result to GUI-Mode

After a CMX-mode execution has been completed, the result can be imported into the GUI environment for inspection and further processing.  To load the result (as in the above example), activate the Open button (icon) above the Reconstruction Parameter group, and the program will prompt to open a CMX file and import the data automatically.  At the end, the system will be restored to exactly the same state as that of a GUI-mode operation.