Subboxing for ChimeraX. Open a cryoEM map with a complex symmetry, crop a monomer, and place the monomers in the parent map. Apply the corresponding transformations to a particle starfile. Inspired by Alister Burt's napari-subboxer.
Demonstration: subboxing a 13-protofilament microtubule
Turn nice map into much nicer map by subboxing your symmetry!
Download ChimeraX_Subbox-1.3-py3-none-any.whl and, in ChimeraX:
toolshed install /path/to/ChimeraX_Subbox-1.3-py3-none-any.whl
Then open it via Tools ▸ Volume Data ▸ Subbox Particles.
- Open your map.
- Crop out a monomer.
- Place duplicates of that monomer onto the corresponding positions in the parent map.
- Point at a star file and press go.
Subbox finds the transform of each monomer relative to the parent map, then for every particle in the input star file writes one output particle per monomer. RELION and Warp/M star files both work. Each offset runs from the parent's box centre (the point the star coordinates refer to) to the monomer's box centre — purely geometric, contour levels play no part. The monomer's box centre is where the sub-particle is centred, so centre the monomer in its box when you crop it.
Each monomer's offset from the parent can be zeroed per axis, which decides whether the output particles stay centred on the complex or move onto the subunit. For a microtubule with the filament axis along Z:
- zero X and Y — the particles are still microtubule segments, just shifted along Z and rotated about the tube axis.
- don't zero them — the particles are now centred on a protofilament. Depending on what you feed them into next, you may need to make a new mask.
© Mart So-Last, 2026 (mgflast@gmail.com)