Directives for Batch Processing and Template Files

Arguments to Copytomocoms
Other Setup Parameters
Preprocessing
Coarse Alignment
Tracking Choices
Beadtracking
Auto Seed Finding
RAPTOR Parameters
Patch Tracking
Patch Track Optimization
Alignment
Tomogram Positioning
Aligned Stack Choices
Aligned Stack Parameters
CTF Correction Parameters
Reconstruction
SIRT Parameters
Tomogram Combination
Postprocessing
Data Set Cleanup
External Commands

Notes:

1. The type entries indicate the kind of data expected to be in the field: one or two integers (separated by a comma), one or two floating point numbers, a boolean value of 0 or 1, or a text string. Text string entries marked as "File" will be shown with a file chooser button in the template editor in Etomo.
2. Template directives must either specify absolute paths or have just a filename with no path. In the latter case, the files are sought in their default locations:
   • A scope template file is expected to be in $IMOD_CALIB_DIR/ScopeTemplate.
   • For a system template, the program looks in $IMOD_CALIB_DIR/SystemTemplate, and if the file is not there, it looks for it in $IMOD_DIR/SystemTemplate. Thus, a customized file placed in the IMOD_CALIB_DIR location will override a file of the same name distributed with IMOD.
   • A user template file is expected to be in the user's selected template directory, which is $HOME/.etomotemplate by default and can be changed in the Settings dialog in Etomo.
3. Template and batch directive filenames must end in the extension ".adoc".
4. Rules for the treatment of directives and the format of values are described in the man page for Batchruntomo. Some essentials are:
   • Directives are processed in order from scope template, system template, user template, and batch directive files, and later entries override earlier ones.
   • All boolean directives must have either a 0 or a 1 after the equals sign, to turn the option off or on.
   • For all other kinds of directives, it is possible to have no value after the equals sign, which means that the parameter in question is not set, even if it was set by an earlier directive. In the case of a "comparam" directive, an empty value will cause the parameter to be removed from the command file.
   • For more details on the effects and possible values of "comparam" directives, consult the man page for the specific program. For more details on the operations controlled by "runtime" directives, see the man page for Batchruntomo.
5. Directives marked with Y in the Tmplt column can be included in a template file. These and all other directives have an effect when the relevant step is run by Batchruntomo. The entry in the Etomo column determines whether they have an effect when running the relevant step for the first time in Etomo as well as the behavior of the directive editor.
6. The entry in the Etomo column has these meanings:
   • SD: Saved by default into a directive file by the directive editor, and will have an effect when running in Etomo.
   • SO: Optionally saved into a directive file by the directive editor, and will have an effect when running in Etomo.
   • Blank: Not saved into a directive file by a directive editor, or not visible by default in a directive editor but optionally savable, and will have an effect when running in Etomo.
   • NE: Will not (yet) have any effect if running in Etomo, and either not saved by a directive editor or not visible by default in a directive editor.
   • NES: Will not (yet) have any effect if running in Etomo, but optionally saved into a directive file by a directive editor.
7. "BRT default" refers to a default value applied by Batchruntomo. "Etomo batch default" refers to a default value that the Etomo batch interface obtains from IMOD/com/batchDefaults.adoc.
8. When doing dose weighting with an ".mdoc" file or an HDF file from SerialEM, no entry is needed for the dose information file except in one case: when processing in the old naming style with an original extension other than ".mrc". In that case, add the directive with just the extension before the ".mdoc" in the name, e.g., ".st".
9. Directives to run a command in place of or after a given step have these rules:
   • The command must be a non-compound command with no redirection, capable of being run as a line starting with $ in a command file.
   • A command to replace a step will be run unconditionally, even if directives are not entered that would cause that step to run ordinarily.
   • A command to run after a step will be run only if that step runs.
   • The string %{setname} will be replaced with the root name of the data files, including the axis letter for dual axis.
10. Until the dose-symmetric entry is supported in Etomo, the dose-symmetric directives cannot be used with tilt series having "bidir=" in the title line unless you turn off Scan Header and provide axis rotation and pixel size entries. Upgrade SerialEM to 3.8.15 or higher to avoid this problem.