Data Processing Tutorials

Tutorials on how to use CryoSPARC jobs and processing cryo-EM data.

Case Studies

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.

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.

Pseudosymmetry in TRPV5 and Calmodulin

Processing EMPIAR-10256 with a focus on handling pseudosymmetry and 3D Classification parameter choices.

End-to-end processing of an inactive GPCR

Processing EMPIAR-10668 including Local Refinement, 3D Variability Analysis, 3D Flex and classification of continuous heterogeneity.

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.

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.

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.

Yeast U4/U6.U5 tri-snRNP

Processing EMPIAR-10073 with a focus on Local Refinement.

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.