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Command-Line Sequence Specification

Certain commands (blastprotein, modeller, etc.) allow specifying a sequence from a ChimeraX Sequence Viewer window. The “alignment” in the window may contain one or more sequences.

The sequence is specified by alignment ID, as reported in the title bar of the Sequence Viewer window, and the name or index number of the sequence in the alignment, in the form:


... enclosed in quotation marks if alignment-ID or sequence-ID includes spaces. The alignment-ID (and even the colon) can be omitted if only one Sequence Viewer window is open. The alignment-ID is generated automatically based on the input unless specified by the user with the ident option of the open command.

The index number can be a positive integer N for the Nth sequence in the alignment, or negative for the Nth-to-last sequence. For example,


specifies the next-to-last sequence in alignment super8.msf. The alignment ID and colon (:) can be omitted if only one alignment is open or the sequence name given is unique across all alignments.

See also: command usage conventions

UCSF Resource for Biocomputing, Visualization, and Informatics / October 2023