Hi Tim, (1) Of course, the specifiers must be correct for the atoms and/or centroids in your structure. You probably have that right but I can't check it because I don't have your exact data. (2) The "distance" command to show the distance does not have a setDefaults option. To use that option you have to use a separate "distance style" command. This is shown in the usage lines on the "distance" help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> Since you are not setting defaults, it will probably work if you just omit the "setDefaults false" part. 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 Feb 1, 2026, at 7:37 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

What is wrong with this second line: define centroid #1/A:214@CD1, CD2, CE1, CE2, CG, CZ radius 0.075 distance #1.3 #1/V:38@NE2 setDefaults false color black dashes 6 radius 0.04

- Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

The "distances" features is meant to show a distance with a label that potentially updates if the distance is changed, aka a distance monitor... if you wanted to just draw a line (pseudobond) you could use "pbond" instead: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/pbond.html> You can remove all distance monitors with command: ~dist With just an unlabeled pseudobond, you could see the distance by pausing the cursor over the pseudobond, and the pop-up balloon label will display it. I hope this helps, Elaine

On Feb 1, 2026, at 8:19 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks, That works! Is there a way to avoid displaying the label or do I just have to close or hide it?

- Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

On Sun, Feb 1, 2026 at 10:59 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Tim, (1) Of course, the specifiers must be correct for the atoms and/or centroids in your structure. You probably have that right but I can't check it because I don't have your exact data.

(2) The "distance" command to show the distance does not have a setDefaults option. To use that option you have to use a separate "distance style" command. This is shown in the usage lines on the "distance" help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>

Since you are not setting defaults, it will probably work if you just omit the "setDefaults false" part.

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 Feb 1, 2026, at 7:37 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

What is wrong with this second line: define centroid #1/A:214@CD1, CD2, CE1, CE2, CG, CZ radius 0.075 distance #1.3 #1/V:38@NE2 setDefaults false color black dashes 6 radius 0.04

- Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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