Hi Nan, There is no option to show a pseudobond such as a distance measurement when the end atoms (or centroids) are hidden. However, you can make the end atoms (or centroids) very small and/or transparent. You can select them by Ctrl-click on one and Shift-Ctrl-click on the other. When both of them are selected as shown by green outline, then use menu Actions... Inspect to open the Selection Inspector. (Another way to open Selection Inspector is by clicking the green magnifying glass icon on the top bar.) See: <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html> In the Selection Inspector when atoms are selected, you can (a) change the atom radius value to very small (make sure the atom style is ball or sphere, not stick; if stick the radius has no effect) - and/or - (b) click the color square to use the system color chooser, in which there is some way to make the color 0% opaque = 100% transparent. Probably (b) transparent is better if you really don't want to see anything at all. However, if small size is OK, you can specify a small radius with "define centroid" tool or command -- then you wouldn't have to change it in a separate step. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html#define-centro...> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> 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 Jun 11, 2025, at 7:50 AM, Nan Zhang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX Developers, I'm working on visualizing a protein-ligand complex with potential π-stacking interactions. To measure the distance between the centroids of two benzene rings (one in the protein residue, one in the ligand), I used the following workflow: • define centroid1 • define centroid2 • distance centroid1 centroid2 (to measure and show the distance between the centroids) My issue: When I try to hide centroid1 centroid2 to generate a cleaner image showing only the distance measurement (the dashed line and label), hiding the centroid points also automatically hides the distance object. Question: How can I hide only the centroid markers (points) while keeping the distance measurement (the dashed line and its label) visible for visualization? Is there a specific command or GUI manipulation to separate these visual elements? I'd appreciate any guidance on resolving this. Thank you for your help and your excellent tool. Best regards, Nan

Nan Zhang zhangnan@nankai.edu.cn

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