Case Study: Exploratory data processing by Oliver Clarke
Last updated
Last updated
The guides presented here are kindly reproduced from Oliver Clarke, PhD, Assistant Professor of Physiology and Cellular Biophysics at Columbia University. They are friendly, approachable introductions to cryoEM data processing in CryoSPARC with a focus on the exploratory, "try-it-and-see" nature of single-particle analysis.
Both guides cover similar topics, but the 2024 version includes some steps which require CryoSPARC v4.4 or later. Below we directly reproduce the general outline section of each guide. The full guide is available in the linked PDF.
These datasets are intended to provide a lightweight and portable starting point for data processing initiated from either CTF estimation and picking (micrographs) or ab-initio volume generation and classification (particles), which can be easily accommodated even on systems with limited storage and processing power. Both sets of data are relatively small, but large enough to allow for identification and characterization of multiple species over the course of the workshop.
These datasets are intended to provide a lightweight and portable starting point for data processing initiated from either CTF estimation and picking (micrographs) or ab-initio volume generation and classification (particles), which can be easily accommodated even on systems with limited storage and processing power. Both sets of data are relatively small, but large enough to allow for identification and characterization of multiple species over the course of the workshop.
This workshop is intended to provide an introduction to "exploratory" data processing in CryoSPARC - that is, data processing with the goal of quickly identifying, reconstructing and refining the molecular species present in a heterogeneous sample. CryoSPARC is used here, but the same general principles & workflow apply to single particle processing in any software package (the particles and micrographs should be directly importable into RELION - just convert the particle.cs
file to a STAR file using csparc2star.py
in pyem
(see ) and you should be good to go). Note: some parts (e.g. symmetry relaxation) require CS 4.4 or later.
I have included two subsets of data for the first part of the workshop (micrographs and extracted & Fourier cropped particles) derived from a publicly available heterogeneous dataset - , the erythrocyte ankyrin-1 complex purified from digitonin extracts of human red blood cell membranes (PMID: ). For the second part of the workshop, addressing mixed symmetry and pseudosymmetry, I have included subsets of data from (the MlaBDEF complex, PMID: ), as well as (TRPV1-DkTx complex, PMID: ).
This workshop is intended to provide an introduction to "exploratory" data processing in CryoSPARC - that is, data processing with the goal of quickly identifying, reconstructing and refining the molecular species present in a heterogeneous sample. CryoSPARC is used here, but the same general principles & workflow apply to single particle processing in any software package (the particles and micrographs should be directly importable into RELION - just convert the particle.cs
file to a STAR file using csparc2star.py
in pyem
(see ) and you should be good to go).
I have included two subsets of data (micrographs and extracted & Fourier cropped particles) derived from a publicly available heterogeneous dataset - , the erythrocyte ankyrin-1 complex purified from digitonin extracts of human red blood cell membranes.