Hi Sepid, There is a "2dlabels" command for placing arbitrary labels and arrows in XY (appears on top of everything, does not rotate with the structure). So you would first decide on the exact view that you want for your figure, then add the labels/titles with this command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html> Currently there is no GUI for the 2D labels, but you can create/edit each label with the "2dlabels" command with some initial x,y position within the window and then drag them to the desired locations using the "move labels" mouse mode. You can assign "move labels" to the right mouse button (= trackpad + Alt on Windows, trackpad + command key on Mac) by clicking the icon in the Right Mouse tab of Toolbar icons across the top. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> Or you can use the "mousemode" command to assign it to some other button or button combination. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> The alternative approach is to add labels separate from ChimeraX. Namely, save an image file without labels from ChimeraX, and then use some other image-editing app like Gimp or Photoshop to add them. 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 Aug 19, 2025, at 11:44 AM, Mazrouee, Sepideh (NIH/OD) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I had the chance to use ChimeraX recently for aligning some predicted protein 3D structures and it looks wonderful. However, I need to do some labeling of the visualization (including labeling of specific protein domains) and I wasn't sure if such feature exists in the software or there might be a way to make it happen.
I would highly appreciate your help if you could provide me with some online resources to educate myself or join a call with some team members to help us out.
Best regards, Sepid Sepideh Mazrouee, PhD Researcher, Office of Data Science Strategy (ODSS) Office of Director, National Institute of Health (NIH)