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Command: sequence

sequence  chain  chain-spec

sequence  associate  chain-spec alignment-ID:sequence-ID ]

sequencedissociate | disassociate )  chain-spec  alignment-ID

The command sequence chain shows the sequence of the specified biopolymer chain in the Sequence Viewer. Only one structure chain should be specified. See also: sequence file formats, blastprotein, modeller, Molecule Display icon

Sequence-structure association (such as for synchronized selection) occurs automatically, but the commands sequence associate and sequence dissociate (same as sequence disassociate) allow more precise control, for example, of which structure chains are used for header calculations, or forcing or removing associations regardless of whether the number of mismatches would be tolerated by the automatic procedure.

The command sequence associate associates one or more structure chains with a sequence. The target sequence for association is specified by alignment ID, as reported in the title bar of the Sequence Viewer window, and the name or index number of the target sequence in the alignment, in the form:  alignment-ID:sequence-ID  (details...).

Alternatively, the sequence-ID can be omitted to associate each specified structure chain with the the best-matching sequence in the alignment. The alignment-ID can be omitted if only one alignment is open, or if the sequence-ID is also omitted; in the latter case, each specified structure chain will be associated with the best-matching sequence in each open alignment. If either or both are omitted, the colon (:) should also be omitted except in rare cases to disambiguate an alignment and sequence that have the same name.

For sequence dissociate, only the alignment needs to be specified, not an individual sequence, because a structure chain can only be associated with one sequence per alignment.

UCSF Resource for Biocomputing, Visualization, and Informatics / May 2019