CryoSPARC Guide

Job: Volume Alignment Tools

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 main functions of the utility are:
  1. 1.
    To apply an arbitrary rigid transformation (shift and/or rotation) to a 3D volume
  2. 2.
    To align a volume to CryoSPARC's symmetry axis conventions, via a rigid transformation
The utility can also ingest 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 transformed by the same rigid transformation applied to the volume. Note that if both shifting and rotation are performed, then the shifting will occur before the rotation.
The major use cases of this job are in:
  • shifting and/or rotating 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

Re-centering Parameters

  • 3D coordinates of new origin (voxels): provide as comma-separated triplet in voxel-units, indexed from the corner of the volume
  • 3D rotation euler angles (ZYZ): provide as comma-separated triplet in radians. The inputs will be transformed via these Euler angles, following the ZYZ convention. For example, to rotate the inputs by 90 degrees around the Z-axis, the rotation string 0, 0, 1.57 may be used

Symmetry Alignment Parameters

  • 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
    • 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