Archived PDFs and Videos of Training Workshops
- S²C² CryoEM CCP-EM Modeling Workshop November 10-13, 2020
- SSRL/LCLS2020 Stanford Synchrotron Radiation Lightsource (SSRL) and the Linac Coherent Light Source (LCLS) User's Meeting: Cryo-EM of COVID-related Macromolecules - September 28, 2020
- 2020 American Crystallographic Association (ACA) Annual Meeting: WK6 Fundamentals of Single Particle Cryo-EM - August 10-11, 2020
- S²C² CryoEM Image Processing Workshop: cryoSPARC - June 10-12, 2020
- Lecture with Dr. Yifan Cheng, HHMI UCSF (no presentation or recording available) & Dr. Christopher Booth, Amtek: Detection Technologies for Cryo-Electron Microscopy - May 29, 2020
- Lecture with Dr. Robert Glaeser, LBNL: Cryo-specimen preparation, and principles of image phase contrast and phase plate - April 20, 2020
- S²C² CryoEM Modeling Workshop: ChimeraX & Phenix - January 15-17, 2020
- S²C² CryoEM Image Processing Workshop: SCIPION - November 18-20, 2019
- S²C² CryoEM Training for Beginners Workshop - September 11-13, 2019
- S²C² CryoEM Modeling Workshop: ChimeraX & Phenix - July 10-12, 2019
- S²C² CryoEM Image Processing Workshop - March 11-13, 2019
- S²C² CryoEM Training for Beginners Workshop - January 22-25, 2019
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Speaker
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Institution
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Presentation Title
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PPT/Other Materials |
Video
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|---|---|---|---|---|
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Colin Palmer
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CCP-EM
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Lecture: Intro to workshop and CCP-EM
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Kevin Cowtan
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University of York
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Lecture: Automated model building with Buccaneer & Nautilus
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Kevin Cowtan
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University of York
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Tutorial: Buccaneer
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Paul Emsley
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MRC, LMB
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Lecture: Cryo-EM model building with modern Coot
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Paul Emsley
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MRC, LMB
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Tutorial: Coot (part 1)
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Paul Emsley
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MRC, LMB
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Tutorial: Coot (part 2)
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Maya Topf
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ISMB, Birkbeck
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Lecture: Flexible fitting of Atomic Models
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Tristan Cragnolini
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ISMB, Birkbeck
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Tutorial: Flex-EM (part 1)
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Aaron Sweeney
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University College London
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Tutorial: Flex-EM (part 2)
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Andrea Thorn
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University of Würzburg
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Lecture: Finding secondary structure in cryo-EM maps: HARUSPEX
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Rob Nicholls
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MRC, LMB
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Lecture: Refinement against cryo-EM maps
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Rob Nicholls
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MRC, LMB
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Tutorial: Refmac (part 1)
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Rob Nicholls
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MRC, LMB
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Tutorial: Refmac (part 2)
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Ardan Patwardhan
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EMBL-EBI
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Lecture: PDB, EMDB, & Empiar: Public archiving of cryo-EM data
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PPT
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Arjen Jakobi
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TU Delft
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Lecture: Map sharpening tools for cryo-EM density maps
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Arjen Jakobi
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TU Delft
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Tutorial: LocScale
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Agnel Joseph
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CCP-EM
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Lecture: Validation of cryo-EM maps and models
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PPT
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Agnel Joseph
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CCP-EM
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Lecture: Model Validation
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PPT
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Agnel Joseph
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CCP-EM
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Tutorial: Model Validation
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All Speakers
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General Q&A Session
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N/A
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Video
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Speaker
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Institution
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Presentation Title
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PPT/Other Materials
|
Video
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|---|---|---|---|---|
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David Veesler
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Univ. of Washington
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Structural Studies of the SARS-CoV Spike Glycoprotein
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N/A
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David Stuart
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Oxford University & Diamond Light Source
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The use of cryoEM structural information to advance SARS2-CoV-2 biology and therapy
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Goran Kokic
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Max Planck Institute, Göttingen
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Structure of replicating SARS-COV-2 polymerase
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Erica Ollmen Saphire, Adrian Enriquez, Kathryn Hasti
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La Jolla Institute for Immunology
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Antibodies against Emerging Viral Disease
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N/A |
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Rhiju Das, Ivan Zheludev
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Stanford University
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CryoEM of previously unsolvable RNA structures including coronavirus genome elements
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Stephan Wilkens
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SUNY Upstate Medical University, Syracuse
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Targeting Vacuolar H+-ATPase for Antiviral Therapy
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Speaker
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Institution
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Presentation Title
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PPT/Other
|
Video
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|---|---|---|---|---|
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Mark Hezik
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UC San Diego
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Sample Preparation for cryo-EM
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David DeRosier
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Brandeis University
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Image Contrast Theory and Reconstruction
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Alexis Rohou
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Genentech
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Principles of Image Processing
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Andres Leschziner
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UC San Diego
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Determining Structures of Challenging Samples
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Dmitry Lyumkis
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Salk Institute
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Dealing with Resolution Anisotropy and Considerations for High Resolution Structure Determination
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Wah Chiu
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Stanford/SLAC
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Atomic Modeling and the Importance of Validation
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Ali Punjani
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Structural Biotechnology
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CryoSPARC Demonstration/Tutorial
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See June Workshop
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June 10-12, 2020 S²C² CryoEM Image Processing Workshop: cryoSPARC (agenda)(User Interface overview/Day 1 Cryo SPARC Instructions/Day 2 Cryo SPARC Instructions/Q&A Day 1/Q&A Day 2/Q&A Day 3)
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Speaker
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Institution
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Presentation Title
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PPT/Other
|
Video
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|---|---|---|---|---|
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David DeRosier
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Brandeis University
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If Only...
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Ali Punjabi
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Structural Biotechnology
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CryoSPARC (AM) 6/10/20 User Interface overview/Day 1 Cryo SPARC Instructions
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Ali Punjabi
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Structural Biotechnology |
CryoSPARC (PM) 6/10/20
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Ali Punjabi
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Structural Biotechnology
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CryoSPARC (AM) 6/11/20
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PPT1/
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Ali Punjabi
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Structural Biotechnology
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CryoSPARC (PM) 6/11/20
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Stephan Arulthasan
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Structural Biotechnology
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CryoSPARC Architecture & Management
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Ali Punjabi
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Structural Biotechnology
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CryoSPARC (PM) 06/11/20
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see above PPTs
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Greg Pintilie
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Stanford University
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CryoEM Map resolution assessment, validation, visualization and segmentation
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Cathy Lawson
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Rutgers University
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EMDataResource: Structure Data Archiving, Validation Challenges
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Speaker
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Institution
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Presentation Title
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PPT/Other
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Video
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|---|---|---|---|---|
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Yifan Cheng
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HHMI UC San Francisco
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N/A
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N/A
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Christopher Booth
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Ametek
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Detection Technologies for Cryo-Electron Microscopy
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Speaker
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Institution
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Presentation Title
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PPT/Other
|
Video
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|---|---|---|---|---|
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Robert Glaeser
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Lawrence Berkeley National Lab (LBNL)
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Geneal Principles of Phase Contrast and Phase Plates
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Robert Glaeser
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Lawrence Berkeley National Lab (LBNL)
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Single-Particle Grid Preparation
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Speaker
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Institution
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Presentation Title
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PPT/Other
|
Video
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|---|---|---|---|---|
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Tom Goddard, Elaine Meng, Eric Pettersen
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UC San Francisco
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ChimerX-Visualization of CryoEM Maps and Models
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N/A
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Greg Pintilie
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Stanford University
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Segmentation, Rigid Body and Flexible Fitting
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N/A
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Tom Goddard, Elaine Meng, Eric Pettersen
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UC San Francisco
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Refinement of cryoEM maps with Isolde
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N/A
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Tom Goddard
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UC San Francisco
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Publication-Quality Images and Movies
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N/A
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Paul Adams
|
Lawrence Berkeley National Lab (LBNL)
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Phenix Introduction
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Paul Adams
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Lawrence Berkeley National Lab (LBNL)
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Atomic Models from Cryo-EM Data
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see above video
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Pavel Afonine
|
Lawrence Berkeley National Lab (LBNL)
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Structure Refinement
|
see above video
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Paul Adams
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Lawrence Berkeley National Lab (LBNL)
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Model Validation for Cryo-EM
|
see above video
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Pavel Afonine
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Lawrence Berkeley National Lab (LBNL)
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Structure Refinement and Validation Practical
|
see above video
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Nigel Moriarty
|
Lawrence Berkeley National Lab (LBNL)
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Ligands
|
see above video
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Greg Pintilie
|
Stanford University
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Assessment of High Resolution CryoEM Features
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Helen Berman
|
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Validation of Biological Structures
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N/A
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N/A
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Cathy Lawson
|
Rutgers University
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EM Structure Archives, Validation and Challenges
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see above video
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Speaker
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Institution
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Presentation Title
|
PPT/Other
|
Video
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|---|---|---|---|---|
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David DeRosier
|
Brandeis University
|
General principles of cryoEM 3D reconstructions
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Jose Maria Carazo
|
CNB-CSIC
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Basic image processing for EM Part 1&2
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Carlos O Sanchez Sorzano
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CNB-CSIC
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Image Processing Principles
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Yiorgio Skiniotis
|
Stanford University
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Dealing with heterogeneity in single-particle data/examples
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N/A
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Greg Pintilie
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Stanford University
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Model building and map validation
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N/A
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N/A
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September 11-13, 2019 S²C² CryoEM Training for Beginners Workshop (agenda) (Prof. Grant Jensen Videos)
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Speaker
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Institution
|
Presentation Title
|
PPT/Other
|
Video
|
|---|---|---|---|---|
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Juergen Plitzko
|
Max Planck Institute
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EM Basics
|
Video
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Yiorgio Skiniotis
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Stanford University
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Freezing Basics
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Video
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Christopher Booth
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Gatan
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Camera
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Video
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Yee Ting Li
|
SLAC National Accelerator Lab
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eLogbook and data transfer
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N/A
|
N/A
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Robert Glaeser
|
Lawrence Berkeley National Lab (LBNL)
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Radiation Damage
|
Video
|
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Zoltan Metlagel
|
FEI
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EPU and Phase Plate
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N/A
|
N/A
|
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Corey Hecksel
|
Stanford University
|
Data Collection (Seriel EM)
|
Video
|
July 10-12, 2019 S²C² CryoEM Modeling Workshop: ChimeraX & Phenix (agenda) (Properly Weighted Map T20S/Model Validation Tutorial/Model Optimization Tutorial)
|
Speaker
|
Institution
|
Presentation Title
|
PPT/Other
|
Video
|
|---|---|---|---|---|
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Todd Goddard, Elaine Meng, Eric Pettersen
|
UC San Francisco
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ChimeraX - Visualization of cryoEM maps and models
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Video
|
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Greg Pintilie
|
Stanford University
|
Rigid Body and Flexible Fitting
|
Video
|
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Paul Adams
|
Lawrence Berkeley National Lab (LBNL)
|
Phenix Introduction
|
Video
|
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Paul Adams
|
Lawrence Berkeley National Lab (LBNL)
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Automated Model Docking and Building
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Video
|
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Pavel Afonine
|
Lawrence Berkeley National Lab (LBNL)
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Phenix Tools for CryoEM: Refinement and Validation
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Video
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Paul Adams
|
Lawrence Berkeley National Lab (LBNL)
|
Model Validation for Cryo-EM
|
Video
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Nigel Moriarty
|
Lawrence Berkeley National Lab (LBNL)
|
Restraints in Phenix
|
Video
|
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Corey Hyrc
|
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Accurate representation of cryoEM Structures
|
Video
|
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Greg Pintilie
|
Stanford University
|
Assessment of High Resolution of CryoEM Features
|
Video
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|
M Robertson
|
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CryoEM Structure Ligand Modeling
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N/A
|
Video
|
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Cathy Lawson
|
Rutgers University
|
CryoEM Archives, Challenges and Validation
|
Video
|
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Speaker
|
Institution
|
Presentation Title
|
PPT/Other
|
Video
|
|---|---|---|---|---|
|
David DeRosier
|
Brandeis University
|
General principles of cryoEM image reconstruction
|
Video
|
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Yee Ting Li
|
SLAC National Accelerator Lab
|
Data acquisition and pre-processing software logging on and computer basics
|
Video
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Cornelius Gati
|
SLAC National Accelerator Lab
|
Image processing with Relion - Introduction
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N/A
|
N/A
|
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Greg Pintilie, Wah Chiu
|
Stanford University
|
Map visualization and validation
|
Video
|
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Cathy Lawson
|
Rutgers University
|
Cryo-EM Map Challenge, Map Deposition and Archiving
|
Video
|
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Yiorgio Skiniotis
|
Stanford University
|
Dealing with heterogeneity in single-particle cryoEM data
|
Video
|
|
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Cornelius Gati
|
SLAC National Accelerator Lab
|
Different image processing software packages
|
N/A
|
N/A
|
| Speaker | Institution | Presentation Title | PPT/Other | Video |
|---|---|---|---|---|
| Yiorgio Skiniotis | Stanford University | Cryo-Specimen Preparation | PPT | N/A |
| Wah Chiu | Stanford/SLAC | Radiation Damage in CryoEM | PPT | N/A |
| Christopher Booth | Gatan | Detection Technologies for Cryo-Electron Microscopy | PPT | N/A |
| Juergen Plitzko | Max Planck Institute | TEM basics and column alignment | PPT | N/A |
| David Bushnell | Stanford/SLAC | Low dose imaging via Serial EM and EPU | PPT | N/A |
| Wah Chiu | Stanford/SLAC | Image contrast theory in CryoEM | PPT | N/A |
| John Spear | Thermofisher | Krios and Talos alignment | PPT | N/A |
| Yee Ting Li | SLAC National Accelerator Lab | eLogbook, data collection monitoring and pre-processing | PPT | N/A |
