> For the complete documentation index, see [llms.txt](https://guide.cryosparc.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-reconstruction-only.md). # Job: Heterogeneous Reconstruction Only ## At a Glance Produce a 3D volume for each class from particle images that were previously classified in an upstream job, using the images’ existing pose estimates and class assignments. ## Description Heterogeneous Reconstruction Only produces a map for each class from a particle stack, using the particles’ existing pose estimates and class assignments. No alignment is performed. This is most often used to produce full-size maps of classes from jobs like [Heterogeneous Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-refinement), which downsample particle images by default. {% hint style="warning" %} Jobs which align and classify particles (like Heterogeneous Refinement and Ab-Initio Reconstruction) do not perform gold-standard half set alignment. Thus, although Heterogeneous Reconstruction Only produces FSC curves, they may overestimate the maps’ resolution. Particles from each class can be refined in a job like [Homogeneous Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-homogeneous-refinement) which does use half set alignment before peforming any tasks for which resolution estimates are important (for instance, model building). {% endhint %} ## Inputs ### Particles (all classes) One or more “all particles” particle stacks which will be reconstructed. These particles must have pose and class estimates (`alignments3D_multi` slot). Note that all particles should have poses and class assignments for a common reference (e.g., they should all come from the same refinement or classification). If particles come from different classification jobs, they will be mixed together and produce unexpected results. You must use the “all particles” output of the upstream job (e.g., Heterogeneous Refinement, Ab-initio Reconstruction, 3D Classification, etc.), which contains information about the particles’ probability of belonging to each class. If you want to reconstruct a subset of classes, using [Homogeneous Reconstruction Only](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-homogeneous-reconstruction-only) once for each class may be preferred. ### Static mask If provided, this mask will be used for FSC calculation. FSC masks are typically tighter than refinement masks, so the Resolution Mask is typically the correct choice from among the masks produced by an upstream refinement. If not provided, a mask is generated using [the same procedure as in a refinement](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-dynamic-masking-in-refinements-v5.0). This generated static mask can optionally be auto-tightened by turning on `Optimize FSC mask`. ## Commonly Adjusted Parameters ### Reconstruction box size (voxels) Box size of the reconstructed volume. By default, volumes are produced with the same box size as the input particle stack. ### Force hard classification By default, a particle’s contribution to a class is proportional to its probability of belonging to that class. If `Force hard classification` is turned on, particles only contribute to the map of their most likely class. Note that if the *upstream classification* was performed with hard classification turned on, the particles will already have probability 1.0 in the most likely class and probability 0.0 of belonging to any other class, so this setting will have no effect. ### Symmetry This symmetry will be applied to the particles during reconstruction. Note that the particles are not aligned to a symmetry axis, so if the previous poses were not found with enforced symmetry this setting may produce unexpected results. See [Symmetry in CryoSPARC](https://guide.cryosparc.com/symmetry-in-cryosparc) for CryoSPARC's symmetry conventions. ### Helical symmetry If the input particles are helical, then `Helical twist (degrees)`, `Helical rise (Angstroms)`, and `Helical symmetry order to apply` must all be entered. These values can be found in the [Helical Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/helical-reconstruction-beta/job-helical-refinement-beta) job card or at the bottom of a Helical Refinement job’s Event Log. ### Force re-do half-set split If this parameter is turned on, particles will be re-assigned to half sets before the volumes are reconstructed. If particles do not have half-set assignments they will be split regardless of this setting. ### Flip the reconstruction hand During the early stages of a refinement, there is no way to determine the handedness of particle images. Maps may therefore be the mirror image of the true volume. Turning on `Flip the reconstruction hand` reassigns particle poses such that they match the mirror image of the original reference. This has the effect of reflecting the maps along the Z-axis and adjusting the particle poses to match. ### Ignore higher-order CTF parameters `Ignore tilt`, `Ignore trefoil`, and `Ignore tetra` each turn off the indicated higher-order CTF correction. This is a quick way to assess the relative contributions of each of these corrections to the final map quality. ### Ewald sphere correction The Ewald sphere (EWS) corrects for the fact that cryo-EM particles have thickness and, thus, slightly varying defocus along the Z-axis. In general, this correction is only necessary for large objects which refine to very high resolution. More information is available in the [Ewald Sphere Correction tutorial](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-ewald-sphere-correction). #### Do EWS correction If this parameter is turned on, the projection will correct for the EWS. #### EWS Curvature sign The EWS can have either positive or negative curvature. There is no practical way to know which is correct *a priori*. In general, we recommend that EWS curvature is determined for a single class using [Homogeneous Reconstruction Only](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-homogeneous-reconstruction-only). ### Optimize FSC mask If this parameter is turned on, the FSC mask’s tightness is optimized to find the best GSFSC resolution, as in [Homogeneous Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-homogeneous-refinement) or [Non-Uniform Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-non-uniform-refinement-new). ### Wide mask final output If this setting is turned on, a wide mask will be applied to the map. This sets many voxels to exactly 0, which makes the compressed size of the file smaller. The uncompressed file (i.e., the .mrc file that you download) will be the same size regardless of this parameter’s value. The magnitude of this effect depends on how much of the box is occupied by solvent. Because web browsers download large files using compression, turning this parameter on also makes volume downloads faster. ### Output zipped half-maps By default, Heterogeneous Reconstruction Only saves only unsharpened and sharpened maps for download. Turning this parameter on also saves each class’s half maps. Note that some classification jobs (notably [Heterogeneous Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-refinement)) do not obey gold-standard half set independence, so care must be taken when using these half maps downstream. ## Outputs ### Particles The input particles. If [`Flip the reconstruction hand`](#id-2a14324a-3a7b-800b-bf31-f827438a11d2) is turned on, the particle poses will be adjusted to match the flipped volume. Otherwise, they are unchanged ([`Force hard classification`](#id-2a14324a-3a7b-800d-9689-f2ad4095a1f8) is only used for reconstruction; the particle probabilities remain the same as the input regardless of this parameter setting). ### All volumes A single [Volumes group](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-split-volumes-group#volumes-groups) containing the reconstructed volumes. ## Recommended Alternatives If reconstructions of a subset of a job’s classes are needed, using a [Homogeneous Reconstruction Only](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-homogeneous-reconstruction-only) for each desired class may be more desirable. We recommend using Homogeneous Reconstruction Only on a single refinement’s particle stack to determine the [Ewald sphere curvature](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-ewald-sphere-correction). Note that most jobs in CryoSPARC begin with a downsampled map, so reconstructing at the full box size is usually not necessary except for visual inspection/presentation.