I'm not sure what you asking. If C1, C2, C3 all have coordinates 0,0,z then they all lie on the same line. Three carbons of a benzene ring don't lie on the same line. Maybe you mean you want 3 atoms to lie in the xy plane, ie have coordinates x,y,0. To do that define a plane for those 3 atoms then use the Structure Measurements panel that will appear to align its normal perpendicular to the screen, or use the command to do that.

On Jun 3, 2025, at 9:00 AM, Alexander Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX community,

I have an optimized benzene ring that's floating in space. Is there a way to align that ring to one of the axes' planes so that 2 of the 3 cartesian coordinates read 0,0?

Ex:

C1 0.00 0.00 z1
C2 0.00 0.00 z2
C3 0.00 0.00 z3

etc

Regards,
Alex
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