WikiSysop: Created page with "== Citation == DiIorio, Megan C. / Kulczyk, Arkadiusz W. A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion...."

2022-06-09T14:49:54Z

Created page with "== Citation == DiIorio, Megan C. / Kulczyk, Arkadiusz W. A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion...."

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== Citation ==

DiIorio, Megan C. / Kulczyk, Arkadiusz W. A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion. 2022. Journal of visualized experiments: JoVE, No. 179.

== Abstract ==

Recent advances in both instrumentation and image processing software have made
single-particle cryo-electron microscopy (cryo-EM) the preferred method for structural
biologists to determine high-resolution structures of a wide variety of macromolecules.
Multiple software suites are available to new and expert users for image processing
and structure calculation, which streamline the same basic workflow: movies acquired
by the microscope detectors undergo correction for beam-induced motion and contrast
transfer function (CTF) estimation. Next, particle images are selected and extracted
from averaged movie frames for iterative 2D and 3D classification, followed by
3D reconstruction, refinement, and validation. Because various software packages
employ different algorithms and require varying levels of expertise to operate, the 3D
maps they generate often differ in quality and resolution. Thus, users regularly transfer
data between a variety of programs for optimal results. This paper provides a guide for
users to navigate a workflow across the popular software packages: cryoSPARC v3,
RELION-3, and Scipion 3 to obtain a near-atomic resolution structure of the adenoassociated
virus (AAV). We first detail an image processing pipeline with cryoSPARC
v3, as its efficient algorithms and easy-to-use GUI allow users to quickly arrive at a
3D map. In the next step, we use PyEM and in-house scripts to convert and transfer
particle coordinates from the best quality 3D reconstruction obtained in cryoSPARC
v3 to RELION-3 and Scipion 3 and recalculate 3D maps. Finally, we outline steps for
further refinement and validation of the resultant structures by integrating algorithms
from RELION-3 and Scipion 3. In this article, we describe how to effectively utilize three
processing platforms to create a single and robust workflow applicable to a variety of
data sets for high-resolution structure determination.

== Keywords ==

== Links ==

https://www.jove.com/es/v/63387/a-robust-single-particle-cryo-electron-microscopy-cryo-em-processing

== Related software ==

== Related methods ==

== Comments ==

2022DiIorio Multiple - Revision history

WikiSysop: Created page with "== Citation == DiIorio, Megan C. / Kulczyk, Arkadiusz W. A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion...."