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Command Usage Conventions

Command help pages have Usage lines that show syntax and options using various fonts and symbols:

See also: help, usage, color specification

The brackets, vertical bars, and parentheses in the Usage lines are merely symbolic and should not be included in the typed command.

Command names and keywords can be truncated to unique strings, with rare exceptions specifically noted. Command names should be entered as lowercase letters, whereas keywords can be completely lowercase or capitalized as shown in the documentation, typically camelCase for compound words. If a truncation matches multiple keywords but one is a simpler compound (for example, silhouettes rather than silhouetteWidth in the set command), the simpler compound is used; otherwise, an ambiguity error is raised.

Boolean (truth) values can also be truncated, with synonyms for true: True, 1, and synonyms for false: False, 0.

Substituting the word browse for a file or directory pathname brings up a file browser window for specifying the name and location interactively. Alternatively, dragging and dropping the icon for a file or directory into the Command Line Interface substitutes the corresponding pathname text.

The display is updated as needed when a user presses return after entering a command, or when a wait command is executed within a script. Multiple commands can be combined into a single line with semicolon separators. During interactive command entry, this may be useful for making multi-frame actions start simultaneously or for suppressing the display of intermediate states. Semicolon separators are also needed for defining composite (multi-command) actions with alias or perframe, whether interactively or in a script.

ChimeraX Command Files

ChimeraX command files are plain text files containing the same commands that could be entered into the Command Line Interface. In addition, they may contain blank lines and/or comments (text with # as the first nonspace character in a line, or in-line with # as the first nonspace character following a semicolon). The filename suffix .cxc is recommended.

Opening a ChimeraX command file in ChimeraX executes the commands. See also: open

UCSF Resource for Biocomputing, Visualization, and Informatics / October 2017