Hi Yanhe,
It's in the distance units of your data, which is usually angstroms.  Markers are basically fake atoms so you can use any of the same methods to set transparency as for atoms.  There are probably several ways, but one way is to select the marker and then use the "transparency" command with "target a", e.g.

transparency sel 50 targ a

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>

Or if you're using the "marker" command to create the marker, you can specity a transparent color in the first place, e.g.

marker #2 position 165.1,162.5,297.1 color 100,100,0,50 radius 10

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.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 Jul 5, 2024, at 3:51 PM, Yanhe Zhao via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX community,
>
> I thought the radius of marker is in angostrom, right? And is that possible to set the transparency of the marker?
>
> Thanks and cheers,
> Yanhe