On May 7, 2026, at 2:11 AM, Wendy Lera via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello Tom,

Thanks for the detailed explanation. I will try shifting the origin index of the map as you suggested and see if that helps with the centering issue.

When I said 'several layers', I meant the structure shows nine molecules per layer, connected by a helical rotation of nearly 120° (~118°) and a rise of ~4.8/3, i.e. ~1.6 Å.

There are three molecules near the center (related by helical symmetry) and three pairs of molecules located between each of the “central” molecules. Thus, 3 + 2×3 = 3 + 6 = 9.

To make it more visual :