ChimeraX Recipes

Align map symmetry axis with z

Tianyang Liu asked on the ChimeraX mailing list how to take a C2 symmetric map with symmetry axis that does not align with x, y, or z axes and make a new map so the symmetry axis aligns with the z axis. To do this you resample the map on a new 3d grid where the z-axis is parallel the symmetry axis. This resampling is going to reduce the quality of the map, so I don’t advice it. Instead you the cryoEM single-particle reconstruction software should put the symmetry axis on the z-axis if you want to preserve map quality. But here is an example how to do the resampling in ChimeraX if you want to.

In this example I make the map from atomic model PDB 7qa1 which has symmetry axis approximately along the xy diagonal. I find the symmetry axis by making two copies of the map, rotating one copy 180 degrees about the approximate axis and fitting it to the first copy. Once I know the axis direction I tilt one of the copies to make the axis along z, then I center it at 0,0,0 and resample it on a new grid at a slightly finer grid spacing. Here are the commands I used. It is a rather tedious process – there is no special ChimeraX command to do this realignment.

open 7qa1
molmap #1 3 gridSpacing 0.8
close #1
volume copy #2
turn 1,1,0 180 model #2
fit #2 in #1
> Axis -0.72099508 -0.69293944 0.00101434
turn 0.69293944,-0.72099508,0 89.942 models #2 coordinateSystem #1
volume new size 256,256,256 gridSpacing 0.5 origin 0,0,0
volume #3 showOutlineBox true
volume #3 originIndex 127.5,127.5,127.5
measure center #2
> Center of mass xyz scene coordinates for 7qa1 map 3 = (8.81, -11.79, -28.81)
move -8.81,11.79,28.81 models #2 coordinateSystem #3
volume resample #2 onGrid #3
save aligned.mrc models #4

The rotation by 89.942 degrees was from acos(0.00101434), the arc-cosine of the z component of the symmetry axis unit vector z component. The tilt is done about axis -vy,vx,0 in the xy plane which is perpendicular to the symmetry axis vx,vy,vz.

Original map with symmetry axis along xy diagonal.

New map with symmetry axis along z.

Tom Goddard, May 22, 2023