Hello, It is possible you accidentally clicked something or chose something from the menu that made it go away. In that case you could try just getting it from the ChimeraX menu again, e.g.

Tools... Command Line Interface

...if it is already listed in the top level of that menu, or if not, then:

Tools... General... Command Line Interface

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

On Apr 12, 2022, at 7:57 AM, Tristan Croll via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Are you sure it's actually missing? Sometimes when you do something that adds a lot of panes to the side panel (e.g. opening a few maps, each of which creates its own Volume Viewer instance), the ChimeraX window can resize to push the command line off the bottom of the screen. Try hitting the maximize button in the corner of the ChimeraX window (or just manually resize/move it) and see if that makes the command line reappear.

From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of mhc128--- via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: 12 April 2022 13:00 To: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Command line disappared

Hello, I am currently completing a project requiring use of ChimeraX. I'm new to the program, and somehow the command line itself has disappeared for me. I have looked throughout the help section but could not find anything specific on re-enabling the use of the command line. Is there anything I am missing?

Thanks for your time.

Hi Steve, (1) there are multiple ways to hide these, but one way is to look in Model panel, use the disclosure triangle on the top-level model to list the "chain trace" submodel. You can uncheck its "Shown" box, or you can close it. After you do whichever one you want, look in the Log to see the equivalent command in case you prefer to use a command in the future.

(2) yes you can rainbow a subset of the chain, exactly as you said. Did you try that command? If it didn't work how you wanted, get a newer ChimeraX version. This capability was added in November 2020. https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

(3) sorry no, there is no separate helix inside color for ribbons in ChimeraX currently... there is a ticket to add it: https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1719

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

On Apr 12, 2022, at 9:14 AM, Steve Chou via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Dear ChimeraX users,

Question 1: When I display the C-alpha atoms in a helix as spheres, I always get lines connecting these atoms. Is there a way to remove/hide the lines? show /A:1-15@CA target a

Question 2: Is it possible to just color a helix, not a whole chain, in a rainbow? rainbow /A:1-15@CA By default, the rainbow spans the whole chain (residues 1-200), and residues 1-15 are colored from red to orange. Is it possible to color residues 1-15 from red to blue?

Question 3: Is it possible to color a helix in two colors - the outside (e.g., red) and inside (e.g., white) in different colors?

Many thanks in advance! Steve