# Job: 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](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/split-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


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