Here are some tips. Your map is 512 by 512 by 512 grid points. If you set the threshold to a level where the noise surrounding the structure is hidden save 0.03 (ChimeraX command "volume level 0.03") then you can measure the center points using ChimeraX command "measure center #1" which show the center of the contour surface is at grid point 256,256,256. So setting that ("volume #1 originIndex 256") will put x,y,z = 0,0,0 at that grid point and the symmetry axis should go through that point. To measure more precise helical rotation and rise you can use the ChimeraX measure symmetry command with the helix option (
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry) and I get for your map
> Symmetry Fmoc-GFFY.mrc: Helix, rise 1.544, angle 118.5, center 256 256 256, n 1
One way to see how accurate these symmetry parameters are is to open a second copy of your map and rotate the second copy 118 degrees and shift by 1.544 Angstroms and see how well it aligns with the first copy of the map.
turn z 118.5 model #2 center 0,0,0 coord #2
move z 1.544 model #2 coord #2
Below is an image of the two copies superimposed (gray and yellow) and the speckly appearance means the maps are overlapping nearly perfectly (sometimes the gray shows, sometimes yellow because the align so well).
The next step would be to fit in your atomic structures of the asymmetric subunit, sounds like that consists of 3 molecules. Then apply the sym command to each of those to generate an atomic model of the helical filament. If your 3 molecular components are models #3-5 you can combine them into 1 model after you fit them with ChimeraX command combine #3-5. Then you can apply symmetry to that asymmetric subunit with
sym #6 h,1.544,118.5,24,-4 center 0,0,0 coord #1 copies true
Below is an image of what I get using map and asym unit model.
Tom