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Command Usage Conventions

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

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

See also: help, usage, color specification, target specification

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.

Pathname and string values should be enclosed in quotation marks if they contain spaces or characters with special meanings in the command line (#, :, and others). In unquoted pathnames and strings, * (wild card), ? (single-character wild card), and square brackets [ ] enclosing alternative single-character matches can be used, as described here for atom and residue names.

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.

ChimeraX Command Files

ChimeraX command files (scripts) are plain text files containing the same commands as entered into the Command Line Interface. The filename suffix .cxc is recommended. Opening a ChimeraX command file in ChimeraX executes the commands. For example command files, see the ChimeraX feature highlights and example images. See also: open, making movies

Rules and tips:
UCSF Resource for Biocomputing, Visualization, and Informatics / November 2018