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1bzm, 1urt, sequence alignment
Models #1 1bzm and #2 1urt associated with sequences in a multiple alignment, with ChimeraX selection sequence region.

Tool: Sequence Viewer

The Sequence Viewer displays individual sequences and sequence alignments of amino acids and nucleotides, with crosstalk to any associated structures. A sequence file can be opened with the command open, and the sequence of a structure chain can be shown by clicking a link in the Log (in the Chain information table that appears when a structure is opened) or by using the command:

sequence chain  chain-spec

Multiple Sequence Viewer windows can be shown at the same time, and they can be manipulated like other panels in ChimeraX (more...). See also: matchmaker

Colored Boxes (Regions)

Sequence regions are colored boxes or outlines that enclose one or more residue symbols. A single region may contain any number of disjoint and/or abutting boxes. Pausing the cursor over a region (but not directly over a residue symbol) shows its name in a pop-up balloon.

Some regions are created automatically, such as by association with a structure. Regions can also be created manually by dragging within the sequence window. Manually created regions are shown in this color.

The active region is the region most recently clicked or created by dragging. Shift-dragging with the left mouse button adds to the active region, whereas Ctrl-dragging creates a new region and makes it the active region. (On Mac, command key replaces Ctrl.) The active region is indicated with a dashed outline; clicking the active region deactivates it, and clicking a different region deactivates the former active region and makes the new region active. A region with no interior color is only responsive to clicks on its borders.

Sequence-Structure Association

A sequence that arose from a structure's chain information is automatically associated with that chain, with regions for protein structure helices and structure strands. Such sequences are closed when their structure chains are deleted or closed, and they are not automatically associated with other structures.

When sequences and structures are opened independently, a structure chain will be associated automatically with a sequence if their sequences can be aligned without mismatches exceeding 1/10 of the residues in the structure chain. The association and number of mismatches will be reported in the Log. For automatic association,

In the sequence window, regions may be created to show mismatches and missing residues according to the association. If a mismatch or missing residue only occurs in a subset of multiple associated structures, a pink box or gray outline is shown instead.

Further effects of association:

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