The video you refer to has the center of symmetry of the microtubule map at 0,0,0. In your case 0,0,0 obviously is far from the helix axis. The sym command has a "center" option that you could specify to give a point on the helix axis.

But a better approach is to adjust the origin of your helical map so the axis passes through 0,0,0. The volume command has origin and originIndex options that allow you to set the origin for the map. Also ChimeraX menu entry Tools / Volume Data / Map Coordinates provides a pane for setting the origin.

On Mar 28, 2023, at 10:24 AM, Aleck Dwyer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,
I am trying to model a microtubule Cryo-EM map (my first time).in Chimera I was following the example
https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html

I was able to do the example but when using my data I see issues.

The spacing is way off. If anyone has modeled a microtubule in Chimera and/or ChimeraX please let me know..

Thanks,
Aleck

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