Data Set Selection Syntax

Many analysis commands can be used to analyze multiple data sets.

The general format for selecting data sets is:


The ’*’ character can be used as a wild-card for entire names (no partial matches).

  • <name>: The data set name, usually specified in the action (e.g. in ’distance d0 @1 @2’ the data set name is “d0”).
  • <aspect>: Optional; this is set for certain data sets internally in order to easily select subsets of data. The brackets are required. For example, when using ’hbond series’, both solute-solute and solute-solvent hydrogen bond time series may be generated. To select all solute-solute hydrogen bonds one would use the aspect “[solutehb]”; to select solute-solvent hydrogen bonds the aspect “[solventhb]” would be used. Aspects are hard-coded and are listed in the commands that use them.
  • <index>: Optional; for actions that generate many data sets (such as ’rmsd perres’) an index is used. Depending on the action, the index may correspond to atom #s, residue #s, etc. A number range (comma and/or dash separated) may be used.

For example: to select all data sets with aspect [shear] named NA_00000:


To select all data sets with aspect [stagger] with any name, indices 1 and 3:


In ensemble mode, data set selection has additional syntax:


Where <member> is the ensemble member number starting from 0.