Hi Alex, 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. open 241 from pubchem define plane @C1,C2,C3 view #1.1 zalign #1.1 Tom 
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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
