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. To apply an arbitrary rigid transformation (shift and/or rotation) to a 3D volume

  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

  • Re-center to mask center of mass: Activate this to re-center the volume, particles, and mask to the center of mass of the supplied mask. If activated, this will override the value supplied to the "3D coordinates of new center" parameter.

  • 3D coordinates of new center (A or px): provide as comma-separated triplet, relative to the corner of the volume. Should be a string of the form x,y,z with a suffix of either A or px to specify the units (Angstroms or pixels, respectively); no suffix will be interpreted as pixels. If provided, volume will be shifted such that its center is at this location, and particle shifts will be modified to preserve their alignment. Leave blank to do no shifting. Shifting will be done before symmetry alignment, if enabled. Enter as a comma separated triplet, e.g. 120, 100, 135 px

  • 3D rotation euler angles (deg or rad): provide as comma-separated triplet. The inputs will be transformed via these Euler angles, following the ZYZ convention. Will be applied after shift. Should be a string of the form Z,Y,Z with a suffix of either deg or rad to specify the units (degrees or radians, respectively); no suffix will be interpreted as radians. For example, to rotate the inputs by 90 degrees around the Z-axis, the rotation string 0, 0, 1.57 rad 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).

Particle Processing Parameters

  • Reassign UIDs: Actviate this to generate fresh UIDs for the output particles, hence causing CryoSPARC to consider the downstream particles as unique particles from the input. This is necessary if output particles are combined with input particles in the same job, for refining with non-crystallographic symmetry operators or arbitrary symmetry transforms.

    • After UIDs are re-generated, low-level result groups from upstream processing cannot be used to override downstream result groups. The output particles are considered to be distinct from the inputs.

    • Note that all connected result groups from the input particles will be re-outputted as new groups, overriding the passthrough system.


  • 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

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