ChimeraX docs icon

Command-Line Sequence Specification

Certain commands (blastprotein and others) 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 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 / January 2022