> 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-homogeneous-reconstruction-only.md). # Job: Homogeneous Reconstruction Only ## At a Glance

Produce a 3D volume from particle images using the images’ existing pose estimates. ## Description Homogeneous Reconstruction Only produces a map from a particle stack, using the particles’ existing pose estimates. No alignment is performed. There are a few cases in which this job is useful. * Generating a map from particle images imported from outside CryoSPARC * Generating a map from particle images which were resized by [Downsample Particles](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/extraction/job-downsample-particles) or which had their orientations changed by jobs like [Volume Alignment Tools](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-volume-alignment-tools) * Generating full-resolution maps of a single class from jobs like [Heterogeneous Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-refinement) or [3D Classification](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-3d-classification) that may have internally downsampled particles while processing * [Breaking pseudosymmetry](#id-2a04324a-3a7b-80a8-91de-df4014813b81) * [Correcting a map which has the wrong handedness](#id-2a04324a-3a7b-80d9-a394-edbdea282789) * [Testing which Ewald sphere curvature is correct](#id-2a04324a-3a7b-8033-bf1a-fd6972f16355) ## Inputs ### Particles (all classes) One or more particle stacks which will be reconstructed. These particles must have pose estimates (`alignments3d` slot). Note that all particles should have poses relative to a common reference (e.g., they should all come from the same refinement). ### 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. ### Symmetry This symmetry will be applied to the reconstructed volume, unless [`Break symmetry`](#id-2a04324a-3a7b-80a8-91de-df4014813b81) is turned on. Note that the particles are not aligned by this job 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. ### Break symmetry If `Break symmetry` is turned on, particles will be randomly permuted by one of the symmetry group operators. This helps introduce asymmetry in pseudosymmetric maps and is usually used before attempting to break symmetry using symmetry relaxation. More information is available in the [Symmetry Relaxation case study](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-symmetry-relaxation#alignment-and-symmetry-mismatches). ### 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 volume is reconstructed. Note that since poses are not updated, this breaks the gold-standard assumption that half-sets remain independent and is therefore not generally recommended. If particles do not have input 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 map 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 on both of these parameters 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*. Once the curvature is determined in this way, the same curvature can be used for the particle stack moving forward. ### Optimize FSC mask If this parameter is turned on, the FSC mask’s tightness is optimized at the end of the job 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. ## Outputs ### Volume The volume produced by backprojecting the particles in their poses. ### Particles The input particles. If [`Flip the reconstruction hand`](#id-2a04324a-3a7b-80d9-a394-edbdea282789) is turned on, the particle poses will be adjusted to match the flipped volume. Otherwise, they are unchanged. ### FSC Mask The mask used during FSC calculation. ## Recommended Alternatives If you are reconstructing each class from a job which produces multiple classes, like [Heterogeneous Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-refinement) or [3D Classification](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-3d-classification), [Heterogeneous Reconstruction Only](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-reconstruction-only) may be preferable as it reconstructs all classes at the same time.