That sounds like the intentional behavior of  the Sequence Viewer respecting your choice of a dark desktop scheme.  If you change your desktop preferences to use a light color scheme, ChimeraX will use that instead.  You can also force ChimeraX to use a light (white) background for all user interface elements by giving the "--color-scheme light" command line argument when you start ChimeraX (or "--color-scheme dark" to force dark mode).  On many systems, ChimeraX will change it's color scheme dynamically when you change the desktop's color scheme.  I've created a ticket, #20811, for adding a ChimeraX GUI setting to change the startup behavior.  

    HTH,

    Greg

Hi Steve and ChimeraX,

While we're talking about the Sequence Viewer, I have another issue.  In ChimeraX 1.11 the panel on the right (including the sequence viewer) has a white background, but in ChimeraX 1.12, the background is black.  Depending on the computer, I sometimes cannot read the sequence on the sequence viewer, particularly if it is highlighted on a black background.  In 1.12 is there a way to set the background back to white? Thanks for a great program, but sometimes your "improvements" are not.

Sincerely,

Ralph Loring

On Sun, Aug 2, 2026 at 6:56 AM Steven Brawer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

A basic question.

Example with one model.  When I make a partial selection by click-drag in a sequence viewer , which turns the sequence bright green (in the sequence viewer), 

then ctl-click in the background of the graphics window to deselect, that bright green color in the viewer turns brown, as below.

What does this mean? Why does it do this?  How to restore the original coloring?

When I run the command sequence chain /A, it apparently creates a new instance of the sequence viewer (deleting the old instance). This is OK with just one model.

The problem with this is that if I have several models and do this, it  puts the new instance at the bottom of the other sequence viewer instances, so I have to move it if I want the same physical order as in the Model pane. This becomes annoying fast.

Is there a way to restore the original coloring in the sequence viewer without completely replacing the original instance of the sequence viewer with an new instance, and leaving it where it is (in the case of  several models).

Thank you

Steve

PS: I have ransacked the documentation and tried Google, but have not found an answer. This does not mean the answer is not there, only that I missed it or didn't understand it when I saw it.

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