Job: Heterogeneous Refinement

Heterogeneous refinement.

Description

Heterogeneous Refinement simultaneously classifies particles and refines structures from n initial structures, usually obtained following an Ab-Initio Reconstruction. This facilitates the ability to look for small differences between structures which may not be obvious at low resolutions, and also to re-classify particles to aid in sorting.

Input

• Initial models

• Particles

Common Parameters

• Refinement box size (voxels):

• Symmetry: You may wish to enforce a particular type of symmetry during refinement. Common types of symmetry include T (tetrahedral), O (octahedral), I (icosahedral), D (dihedral) and C (cyclic).

• Use spherical mask (new in v4.5): Default is on with a corner window mask. User can control the inner and outer diameter of the mask with parameters Spherical mask diameter (A) and Spherical mask diameter outer (A). If only the inner diameter is set, the outer diameter is default to be 20 percent larger than the inner diameter. The window mask transitions smoothly between inner and outer diameters.

Output

• All particles

• All volumes

  • Note that this is a volumes group output, new in CryoSPARC v4.5. It includes a series result containing a downloadable zip file of all volumes.

• Particles for each class

• Volume for each class

  • Including Half-maps

• Plots, including orientation distribution for each class

Notes

This task enables simultaneously sorting particles and identifying classes and is particularly useful in cases where identified classes look very similar. This task can also be used as a method to remove “junk” particles.

Limitations

The initial models provided must be on the correct grey scale. Outputs from ab-initio reconstruction in CryoSPARC meet this requirement.

Common Next Steps

• Download and inspect map