Thank you. That is helpful. From: Elaine Meng <meng@cgl.ucsf.edu> Date: Friday, January 24, 2025 at 5:26 PM To: Das, Abhinaba <abhinaba.das@emory.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [External] Re: [chimerax-users] Confirming coordinate axis Dear Abhi, You can see a small display of XYZ axes using command cofr show true <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cofr.html> Another way is to open a 3D object containing definitions of solid arrows pointing along X,Y, Z (attached file axes.bild). You can edit that file in a text-editor before opening it to make it bigger, if that helps see the directions along with your map. The bild format is very simple and described here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.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 Jan 24, 2025, at 2:00 PM, Abhinaba Das via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX-users,

I'm writing to ask if there is a way to view the x,y,and z axis live while model building. I've a helical map generated in CryoSPARC which has a D1 symmetry. I could generate the asymmetric unit (ASU) for the corresponding C1 reconstruction but having issues applying D1 symmetry. The approach I've taken is to make a diheral copy of the C1 ASU (turn y 180 center <mapId> coordinateSystem <mapId> model <modelid>; followed by combine command). This should generate the dihedral ASU, and if the helical symmetry is applied should generate the symmetric copies (?). But seems not to be working.. I've assumed that the dyad axis is along the y-axis (cryosparc says for its output map). Just wondering if the axes are aligned..

Thanks, Abhi