Job: Volume Alignment Tools


The Volume Alignment Tools utility is a collection of low-level tools to adjust the position and orientation of volumes and particles in 3D space. The two main functions of the utility are:
  1. 1.
    To shift the 3D origin of a volume
  2. 2.
    To align a volume to point group or helical symmetry axes
The utility can also take in a stack of particles. If particles are supplied to the job, their alignments will be modified in concert with the volume to keep them correctly aligned to the output volume. If a mask is supplied, it will be translated (and rotated, if symmetry alignment is enabled) via the same shift (and rotation) applied to the volume. Note that if both shifting and symmetry alignment are desired, then the shifting will occur before symmetry alignment.
The major use cases of this job are in:
  • shifting the volume and particles to focus on a subunit (for subsequent local refinement, or for re-centering the particles prior to extraction from micrographs)
  • aligning the volume and particles to the correct symmetry axes


  • Volume (required)
  • Mask (optional)
  • Particles (optional)

Common Parameters

  • Coordinates of new origin (comma-separated triplet, indexed from the corner of the volume)
  • Symmetry alignment (if enabled):
    • Symmetry string: C, D, I, O, or T, indicating the desired symmetry group to use for alignment.
    • Helical twist (degrees), rise (Å), and symmetry order.
    • Ignore shifts in symmetry alignment: Activate to prevent searching over shifts during symmetry alignment; this will speed up the job if you know the volume is correctly centred.
    • Verbose: Activate to print intermediate rotation matrices and shifts.

Advanced Parameters

  • Symmetry alignment (search and sampling parameters):
    • Search over all of SO(3): If active, will search over rotations covering all of SO(3), rather than just the asymmetric unit. For higher order symmetries (octahedral or icosahedral), deactivating this can speed up job significantly.
    • Initial Fourier-space radius (voxels in Fourier space): Controls the initial resolution used for symmetry alignment.
    • Maximum alignment resolution (Å): Controls the maximum resolution information used for symmetry alignment.
    • Initial shift extent (voxels): Maximum spatial extent of shifts to search over. May be increased to search over a wider range of shifts.
    • Initial shift grid sampling: Number of initial shift grid points to evaluate (along one axis).
    • Initial rotation grid sampling: Number of initial rotation grid points to evaluate (along one axis).


  • Aligned volume
  • Aligned mask
  • Aligned particles

Common Next Steps

  • Extract from micrographs (may be used to re-extract particles centred on the new origin)
  • 3D Refinement
  • Local Refinement
  • 3D Classification
Last modified 1mo ago