# Data Processing Tutorials ## Case Studies

		Cover image
End-to-end processing of a motor-bound nucleosome part 1	Processing EMPIAR-10739 including handling global pseudosymmetry, using 3DVA to guide classification strategies, separating low population classes, and local refinement of a flexible region.	v4.7.1-EMPIAR-10739-Figure13.png		case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739
Processing of a motor-bound nucleosome part 2	Processing EMPIAR-10739 including using 3DVA to guide classification strategies, separating low population classes, and local refinement of a flexible region.	v4.7.1-EMPIAR-10739-Figure23.png
End-to-end processing of a ligand-bound GPCR	Processing EMPIAR-10853 including Micrograph Denoising, Micrograph Junk Detector, Subset Particles by Statistic, Local Refinement and focussed 3D Classification to improve ligand density.	gpcr.png	case-study-end-to-end-processing-of-a-ligand-bound-gpcr-empiar-10853
DkTx-bound TRPV1	Processing EMPIAR-10059 in CryoSPARC v4.6 with a focus on particle curation, developing an intuition for when a domain may be blurred due to flexibility, and how to handle this type of flexibility.	Untitled.png	case-study-dktx-bound-trpv1-empiar-10059
Pseudosymmetry in TRPV5 and Calmodulin	Processing EMPIAR-10256 with a focus on handling pseudosymmetry and 3D Classification parameter choices.	classify-then-align.png	case-study-pseudosymmetry-in-trpv5-and-calmodulin-empiar-10256
End-to-end processing of an inactive GPCR	Processing EMPIAR-10668 including Local Refinement, 3D Variability Analysis, 3D Flex and classification of continuous heterogeneity.	case-study-card-photos.png	case-study-end-to-end-processing-of-an-inactive-gpcr-empiar-10668
End-to-end processing of encapsulated ferritin	Processing EMPIAR-10716 with a focus on high-symmetry ab-initio reconstruction, local symmetry, non-point-group symmetry, symmetry expansion, and custom geometry operations.	case-study-card-photos.png	case-study-end-to-end-processing-of-encapsulated-ferritin-empiar-10716
Discrete and Continuous Heterogeneity in FaNaC1	Processing a combined dataset of an ion channel with a focus on techniques for separating conformational states from a heterogeneous mixture.	Untitled.png
Picking-induced Orientation Bias in HA Trimer	An analysis of the impact of data collection and particle picking techniques on orientation bias, including strategies for improving map quality and isotropy.	adjacent-topdowns.png	case-study-picking-induced-orientation-bias-in-ha-trimer-empiar-10096-and-10097
Yeast U4/U6.U5 tri-snRNP	Processing EMPIAR-10073 with a focus on Local Refinement.	tri-snRNP_search-extents.png	case-study-yeast-u4-u6.u5-tri-snrnp
Exploratory data processing by Oliver Clarke	Friendly, approachable introductions to cryoEM data processing in CryoSPARC with a focus on the exploratory, "try-it-and-see" nature of single-particle analysis. Kindly reproduced from Oliver Clarke, PhD, Assistant Professor of Physiology and Cellular Biophysics at Columbia University.	Untitled.png	case-study-exploratory-data-processing-by-oliver-clarke
Tips for Membrane Protein Structures	Helpful hints for processing cryo-EM data of membrane proteins.	image.png	tutorial-tips-for-membrane-protein-structures
Common CryoSPARC Plots	A detailed description of the common plots that CryoSPARC makes across multiple job types.	Untitled.png	tutorial-common-cryosparc-plots

## Data Processing Alongside these tutorials, see: [**All Job Types in CryoSPARC**](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc) and [**Tutorial Videos**](https://guide.cryosparc.com/processing-data/tutorial-videos) ### Files, Data and Import {% content-ref url="tutorials-and-case-studies/negative-stain-data" %} [negative-stain-data](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/negative-stain-data) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/phase-plate-data" %} [phase-plate-data](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/phase-plate-data) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-eer-file-support" %} [tutorial-eer-file-support](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-eer-file-support) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-epu-afis-beam-shift-import" %} [tutorial-epu-afis-beam-shift-import](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-epu-afis-beam-shift-import) {% endcontent-ref %} ### Preprocessing {% content-ref url="tutorials-and-case-studies/tutorial-patch-motion-and-patch-ctf" %} [tutorial-patch-motion-and-patch-ctf](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-patch-motion-and-patch-ctf) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-float16-support" %} [tutorial-float16-support](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-float16-support) {% endcontent-ref %} ### Particle Picking {% content-ref url="tutorials-and-case-studies/tutorial-particle-picking-calibration" %} [tutorial-particle-picking-calibration](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-particle-picking-calibration) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-blob-picker-tuner" %} [tutorial-blob-picker-tuner](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-blob-picker-tuner) {% endcontent-ref %} ### Helical Reconstruction {% content-ref url="tutorials-and-case-studies/case-study-empiar-10031-mavs" %} [case-study-empiar-10031-mavs](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-empiar-10031-mavs) {% endcontent-ref %} ### 3D Refinement {% content-ref url="tutorials-and-case-studies/performance-metrics" %} [performance-metrics](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/performance-metrics) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-ctf-refinement" %} [tutorial-ctf-refinement](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-ctf-refinement) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-ewald-sphere-correction" %} [tutorial-ewald-sphere-correction](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-ewald-sphere-correction) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-symmetry-relaxation" %} [tutorial-symmetry-relaxation](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-symmetry-relaxation) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-orientation-diagnostics" %} [tutorial-orientation-diagnostics](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-orientation-diagnostics) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-bild-files" %} [tutorial-bild-files](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-bild-files) {% endcontent-ref %} ### Local Refinement {% content-ref url="tutorials-and-case-studies/mask-selection-and-generation-in-ucsf-chimera" %} [mask-selection-and-generation-in-ucsf-chimera](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/mask-selection-and-generation-in-ucsf-chimera) {% endcontent-ref %} ### Conformational Variability {% content-ref url="tutorials-and-case-studies/tutorial-3d-classification" %} [tutorial-3d-classification](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-classification) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-3d-variability-analysis-part-one" %} [tutorial-3d-variability-analysis-part-one](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-variability-analysis-part-one) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-3d-variability-analysis-part-two" %} [tutorial-3d-variability-analysis-part-two](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-variability-analysis-part-two) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-3d-flexible-refinement" %} [tutorial-3d-flexible-refinement](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-flexible-refinement) {% endcontent-ref %} {% content-ref url="tutorials-and-case-studies/tutorial-3d-flex-mesh-preparation" %} [tutorial-3d-flex-mesh-preparation](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-flex-mesh-preparation) {% endcontent-ref %}