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1bzm, 1urt, sequence alignment
Models #1 1bzm and #2 1urt associated with sequences in an 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. To find and select a specified sequence or sequence pattern, use Select... Sequence in the menu or the select command. See also: matchmaker

The sequence of a structure chain in ChimeraX can be shown by:

Sequences and sequence alignments can also be opened from files or fetched from UniProt.

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

Each Sequence Viewer window has a context menu with choices including:

Headers

Headers are the rows of information above the sequences: consensus sequence, conservation histogram, etc. Which headers are shown and how they are calculated can be controlled in the Headers settings.

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 (default, see Regions settings).

The active region is the region most recently clicked or created by dragging, and is indicated with a dashed outline. 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.) Backspace/delete deletes the active region. 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,

For manual association, both of the above are allowed, but only the “extra” residues in the structure not associated with any positions in the sequence (minus the length difference if the structure sequence is longer) are counted along with mismatches and reported in the Log.

Associations can be controlled manually (forced or removed):

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 (default, see Regions settings).

Further effects of association:

Sequence Viewer Settings (Preferences)

Choosing Settings... from the Sequence Viewer context menu shows its settings in a separate window, with sections:

The settings window can be manipulated like other panels in the ChimeraX interface (more...).

Save saves the current settings as preferences, Reset replaces the current settings with the initial “factory” defaults (values shown in bold below), and Restore restores values that were saved previously. The Buttons below... option indicates whether these buttons should apply only to the currently shown section (e.g., Appearance) or to all of the Sequence Viewer preferences. Although there can be multiple settings windows with different values for multiple Sequence Viewer windows, there can be only one set of saved preference values.

Appearance

Headers

The consensus sequence shows the residue type that is most common at each position in the alignment, even if it appears in less than 0.5 of the sequences; if a consensus type appears in at least the capitalization threshold fraction of sequences, it will be capitalized and shown in purple, or in red if all of the sequences have the same type. If several residue types are equally the most common, one is chosen at random. The consensus will show a gap at positions where a gap is the most prevalent or equally the most prevalent as one or more residue types, unless ignore gap characters is turned on. Regardless of this option, however, gap positions are always included in the denominator for calculating the consensus fraction.

Regions

The Regions section of settings controls whether different types of regions should be shown, and if so, their initial colors. Each color well can be clicked to choose a color interactively. On/off checkboxes indicate whether to color the region border (box outline) and/or interior (box fill), whereas full and partial refer to whether the region applies to all structures associated with a position or to only some fraction of those structures.


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