TRPV1 and a Standard Workflow (Part 2 of 6)

In this video (Part 2 of 6), we present a step-by-step explanation of one possible way to process micrographs of TRPV1 from EMPIAR 10059 (https://www.ebi.ac.uk/empiar/EMPIAR-1.... The jobs presented here define what we call a “standard workflow”, which we expect to produce a workable consensus refinement for most single particle cryo-EM datasets. By no means is this the only (or the best) way to process data! It is merely meant to guide new users through the most common set of jobs, and present ways to handle challenges as they arise. Our standard workflow comprises preprocessing, blob picking, particle curation, template picking, more particle curation, and finally a consensus refinement. We cover each of these steps in detail in the relevant chapters, explaining parameter choices along the way. Additionally, we present some jobs which do not produce the desired result and discuss why they failed. Chapters: 00:00 Introduction and TRPV1 Background 01:58 A Standard Workflow 03:19 Preprocessing 05:36 Blob Picking and Particle Curation 13:41 Extraction and Template Generation 25:24 Template Picking and 3D Particle Curation 30:37 Detecting Junk in a Particle Stack 34:07 Particle Curation with Heterogeneous Refinement 47:52 Q&A: Picking and Curating Particles 54:08 Consensus Refinement 1:02:53 The Effect of Flexibility 1:10:00 Masks and Local Refinement 1:20:02 Final Q&A This video is the second in a series of six recordings covering single particle cryo-EM data processing in CryoSPARC from the 2024 Single-Particle Cryo-EM Image Processing Workshop held by the Stanford-SLAC CryoEM Center (S2C2) in 2024. The original recordings are courtesy of S2C2. Captions were automatically generated by Zoom and may contain errors. Workshop: https://s2c2.slac.stanford.edu/traini... S2C2: https://s2c2.slac.stanford.edu/traini... More tutorials and videos are available in the CryoSPARC Guide: https://guide.cryosparc.com/