Thanks Elaine, that solves it.

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Monday, March 24, 2025 at 3:49 PM
To: Kevin M Jude <kjude@stanford.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Force display of helix with setattr

Hi Kevin,
This is how it looks when they are both "helix" but assigned to two different helices, so an intervening thinner segment is used to indicate they are not in the *same* helix.  However, you can mark them as being in the same helix as one another -- that is another residue attribute, ss_id.

How to control it is covered in more detail in the User Guide and various previous posts.  See for example the following and links therein:

<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/P34Q6R2R3VOGGII7COZE6NWH6K4Q6OE3/>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 24, 2025, at 3:41 PM, Kevin M Jude via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> For some reason the selected residues in this image are not displayed as a helix in ChimeraX. I think the command to force it woud be ‘setattr sel res ss_type 1’, but nothing changes (the log says “Assigning ss_type attribute to 2 items”). Same result if I try ‘setattr sel res is_helix 1’. Can anybody please set me straight (and my cartoons helical)?
>  Using ChimeraX 1.9 for OS X. Thanks for any help.
>   <image001.png> --