etomo(1) etomo(1) NAME etomo - A GUI program to run IMOD and PEET batch programs SYNOPSIS etomo [option ...] [data_file ...] DESCRIPTION Etomo is an interface for running a subset of IMOD and PEET commands. It can be run interactively, with automation, or with a combination of the two. Etomo contain four interfaces: one for doing tomographic reconstructions, one for joining tomograms, one for particle averaging, and one for running a process using IMOD's parallel processing capabilies. Etomo's standard error goes to a dated log file. The name location of the logs are placed in a file called etomo_err.log, which is placed the current directory. When in use, standard out is send to etomo_out.log. OPTIONS --axis single|dual For automation. Sets the Axis Type field in the Setup Tomogram dialog. See USAGE. --create For automation. Pressed the Create Com Scripts button in the Setup Tomogram dialog. See USAGE. --dataset tilt_series_file|dataset_name For automation. Sets the Dataset Name field in the Setup Tomogram dialog. Can be set to a file containing a tilt series or to the dataset name. A dataset name is the root name of the tilt series file, excluding the extension (and the axis extension - "a" or "b" - in the case of dual axis). Must be in the local directory unless the --dir option is used. See USAGE. --debug Send extra information to standard error. The --debug option turns on the following options: --memory and --timestamp. --demo Deprecated. --dir "directory_path" For automation. The absolute or relative directory containing the file or dataset specified with the --dataset option. --exit For automation. Causes etomo to exit after the Setup Tomogram dialog is completed. See USAGE. --fg Used with automation. Must be the first option. Causes etomo to be run in the foreground rather then in the background. This is useful when running etomo with automation from a script; a script will not wait until etomo is done unless etomo is running in the foreground. See USAGE. --fiducial fiducial_diameter For automation. Sets the Fiducial Diameter field in the Setup Tomogram dialog. Fiducial_diameter is a double. See USAGE. --frame single|montage For automation. Selects the Frame Type radio buttons in the Setup Tomogram dialog. See USAGE. --headless For testing. No window is created. Used for unit testing. -h, --help Send a usage message to standard out (goes to the command line not to a file) and exit. --listen Forces all 3dmods to be run with the -L option. This only has an effect on Windows computers because -L is always used on Linux and Mac. When --listen is used in Windows, messages to 3dmod will be sent through stdin rather then imodsendevent. --memory [interval] Log memory usage statements before and after processes are run. The interval is an integer which denotes the interval in minutes at which to send additional memory usage statements. --names Used with testing. Send the names of screen elements to standard out. For writing automated regression tests. --newstuff May cause Etomo to run with unreleased functionality. --scan For automation. Runs Scan Header in the Setup Tomogram dialog. See USAGE. --selftest Causes etomo to do some internal testing. Etomo may run more slowly. --test For testing. Test mode used for unit testing and automated regression testing. --timestamp Send timestamps to standard error before and after processes are run. USAGE Automation Automation will be completed before handing control over to the user. Automation parameters all affect the Reconstruction Setup dialog and should be used without a data file. All automation parameters are optional. The automation parameters will always be executed in the same order. The order in which they appear is ignored, except for --fg, which must be first. Automation parameters are executed in the following order: --fg --dir --dataset --axis --frame --fiducial --scan --create --exit FILES Data Files *.edf Tomographic reconstruction data file. *.ejf Data file for joining tomograms. *.epe PEET data file (particle averaging). *.epp Parallel process data file. Log Files $HOME/.etomologs/etomo_err_timestamp.log Contains the log. The location is configurable (see man imodenv). etomo_err.log Contains the location of the log. Placed in the directory from which etomo is run. etomo_out.log Contains the output of the --names parameter. May also contain diagnostic messages. Placed in the directory from which etomo is run. AUTHOR Sue Held SEE ALSO imodenv, uitest, 3dmod. BL3DEMC 2/12/2009 etomo(1)