Archived PDFs and VIdeos of Training Workshops and Lectures
- 2021 March 3-4, S2C2 CryoEM Specimen Preparation and Data Collection Workshop
- 2020 November 10-13, S2C2 CryoEM CCP-EM Modeling Workshop
- 2020 September 28, 2020 Stanford Synchrotron Radiation Light Source (SSRL) and the Linac Coherent Light Source (LCLS) Users' Meeting: CryoEM of COVID-19 related Macromolecules
- 2020 August 10-11, American Crystallographic Associate (ACA) Annual Meeting: WK6 Fundamentals of Single Particle CryoEM
- 2020 June 10-12, S2C2 CryoEM Image Processing Workshop: cryoSPARC
- 2020 May 29, Lecture: Dr. Yifan Cheng, HHMI UCSF & Dr. Christopher Booth, Amtek
- 2020 April 20, Lecture: Dr. Robert Glaeser, LBNL
- 2020 January 15-17, S2C2 CryoEM Modeling Workshop: ChimeraX & Phenix
- 2019 November 18-20, S2C2 CryoEM Image Processing Workshop: SCIPION
- 2019 September 11-13 S2C2 CryoEM Training for Beginners Workshop
- 2019 July 10-12, S2C2 CryoEM Modeling Workshop: ChimeraX & Phenix
- 2019 March 11-13, S2C2 CryoEM Image Processing Workshop
- 2019 January 22-25, S2C2 CryoEM Training for Beginners Workshop
2021 March 3-4, S2C2 CryoEM Specimen Preparation and Data Collection Workshop
Other Materials: Prof. Peter J. Peters Paper "Understanding the invisible hands of sample preparation for cryo-EM"
| Speaker | Institution | Title | Video | |
|---|---|---|---|---|
| Wednesday, March 3, 2021 | ||||
| Peter J. Peters | (M4i) Maastricht University & CryoSol-World | Understanding the invisible hands of sample preparation for cryo-EM | 1,2,3,4 | |
| Benjamin Bammes | Direct Electron, LP | Optimizing Direct Detector Design for a Range of Cryo-EM Techniques | 1,2,3,4 | |
| Jeffrey Lengyel | Thermo Fisher | The latest generation technology for Cryo-EM allowing for unparalleled scientific breakthroughs | 1,2,3,4 | |
| Thursday, March 4, 2021 | ||||
| Christopher Russo | LMB, MRC, Cambridge UK | Principles of information loss in cryoEM and how eliminating specimen movement can improve cryomicrographs | Video | |
| Sahil Gulati | Ametek | Advances in direct electron detection: getting the most out of your microscope | Video | |
| Yee Ting Li | SLAC National Accelerator | Data Management at S2C2 | Video | |
| Patrick Mitchell | SLAC National Accelerator | S2C2 data collection | Video | |
2020 November 10-13, S2C2 CryoEM CCP-EM Modeling Workshop
Other Materials: agenda, computing instructions
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| Colin Palmer | CCP-EM | Lecture: Intro to workshop and CCP-EM | Video | |
| Kevin Cowtan | University of York | Lecture: Automated model building with Buccaneer & Nautilus | Video | |
| Kevin Cowtan | University of York | Tutorial: Buccaneer | - | Video |
| Paul Emsley | MRC, LMB | Lecture: Cryo-EM model building with modern Coot | Video | |
| Paul Emsley | MRC, LMB | Tutorial: Coot (part 1) | - | Video |
| Paul Emsley | MRC, LMB | Tutorial: Coot (part 2) | - | Video |
| Maya Topf | ISMB, Birkbeck | Lecture: Flexible fitting of Atomic Models | Video | |
| Tristan Cragnolini | ISMB, Birkbeck | Tutorial: Flex-EM (part 1) | - | Video |
| Aaron Sweeney | Univ. College London | Tutorial: Flex-EM (part 2) | - | Video |
| Andrea Thorn | University of Würzburg | Lecture: Finding secondary structure in cryo-EM maps: HARUSPEX | Video | |
| Rob Nicholls | MRC, LMB | Lecture: Refinement against cryo-EM maps | Video | |
| Rob Nicholls | MRC, LMB | Tutorial: Refmac (part 1) | - | Video |
| Rob Nicholls | MRC, LMB | Tutorial: Refmac (part 2) | - | Video |
| Ardan Patwardhan | EMBL-EBI | Lecture: PDB, EMDB, & Empiar: Public archiving of cryo-EM data | - | Video |
| Arjen Jakobi | TU Delft | Lecture: Map sharpening tools for cryo-EM density maps | Video | |
| Arjen Jakobi | TU Delft | Tutorial: LocScale | - | Video |
| Agnel Joseph | CCP-EM | Lecture: Validation of cryo-EM maps and models | Video | |
| Agnel Joseph | CCP-EM | Lecture: Model Validation | - | Video |
| Agnel Joseph | CCP-EM | Tutorial: Model Validation | - | Video |
| All Speakers | General Q&A Session | - |
2020 September 28, 2020 SSRL/LCLS Users' Meeting: Cryo-EM of COVID-related Macromolecules
Other Materials: agenda
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| David Veesler | University of Washington | Structural Studies of the SARS-CoV Spike Glycoprotein | - | Parts 1, 2 |
| David Stuart | Oxford University, Diamond Light Source | The use of cryoEM structural information to advance SARS2-CoV-2 biology and therapy | Parts 1, 2 | |
| Goran Kokic | Max Planck Institute, Göttingen | Structure of replicating SARS-COV-2 polymerase | Video | |
| Erica O. Saphire Adrian Enriquez | La Jolla Institute | Antibodies against emerging viral disease | - | Video Q&A |
|
Rhiju Das
Ivan Zheludev
|
Stanford University | CryoEM of previously unsolvable RNA structures including coronavirus genome elements | Video Q&A | |
| Stephan Wilkens | SUNY Upstate Medical University | Targeting Vacuolar H+-ATPase for Antiviral Therapy | Parts 1, 2, 3 |
2020, August 10-11, ACA 2020 Annual Meeting; WK6 Fundamentals of Single Particle CryoEM
Other Materials: agenda
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| Mark Herzik | UC San Diego | Sample preparation for cryo-EM | Parts 1, 2 | |
| David DeRosier | Brandeis University | Image contrast theory and reconstruction | Parts 1, 2 | |
| Alexis Rohou | Genentech | Principles of image processing | Parts 1, 2 | |
| Andres Leschziner | UC San Diego | Determining structures of challenging samples | PDF 1, 2, 3 | Parts 1, 2 |
| Dmitry Lyumkis | Salk Institute | Dealing with resolution anisotropyand considerations for high resolution structure determination | Parts 1, 2, 3 | |
| Wah Chiu | Stanford/SLAC | Atomic modeling and the importance of validation | Parts 1, 2 | |
| Ali Punjani | Structural Biotechnology | CryoSPARC demonstration/tutorial (see June Workshop for slides) | - | Parts 1, 2, 3, 4 |
2020 June 10-12, S2C2 CryoEM Image Processing Workshop: cryoSPARC
Other Materials: agenda, user interface overview, cryoSPARC instructions Day 1 / Day 2, Q&A Day 1, Day 2, Day 3
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| David DeRosier | Brandeis University | If only... | Parts 1, 2, 3 | |
| Ali Punjabi | Structural Biotechnology | CryoSPARC (AM) 06/10/20 User interface overview/Day 1 CryoSPARC Instructions | PDF 1, 2 | Parts 1, 2, 3, 4, 5, 6 |
| Ali Punjabi | Structural Biotechnology | CryoSPARC (PM) 06/10/20 | Parts 7, 8, 9, 10, 11, 12 | |
| Ali Punjabi | Structural Biotechnology | CryoSPARC (AM) 06/11/20 | Parts 1, 2, 3, 4, 5, 6, 7, 8 | |
| Ali Punjabi | Structural Biotechnology | CryoSPARC (PM) 06/11/20 | Parts 9, 10, 11, 12 | |
| Stephan Arulthasan | Structural Biotechnology | CryoSPARC architecture & management | Video | |
| Ali Punjabi | Structural Biotechnology | CryoSPARC (PM) 06/11/20 | - | Parts 13, 14, 15, 16 |
| Greg Pintilie | Stanford University | CryoEM map resolution assessment, validation, visualization and segmentation | Parts 1, 2, 3 | |
| Cathy Lawson | Rutgers University | EMDataResource: structure data archiving, validation challenges | Part 1, 2 |
2020 May 29, Lecture with Dr. Yifan Cheng, HHMI UCSF & Dr. Christopher Booth, Amtek
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| Yifan Cheng | HHMI UC San Francisco | Basics of sample preparation | - | - |
| Christopher Booth | Amtek | Detection technologies for cryo-electron microscopy | Parts 1, 2, 3, 4, 5, 6 |
2020 April 20, Lecture with Dr. Robert Glaeser, LBNL
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| Glaeser, Robert | Lawrence Berkeley National Lab | General principles of phase contrast and pase plates | Video | |
| Glaeser, Robert | Lawrence Berkeley National Lab | Single-particle grid preparation | Video |
2020 January 15-17, S2C2 CryoEM Modeling Workshop: ChimeraX & Phenix
Other Materials: agenda
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
|
Tom Goddard
Elaine Meng
Eric Pettersen
|
UC San Francisco | ChimeraX-Visualization of cryoEM maps and models | - | |
| Greg Pintilie | Stanford University | Segmentation, rigid body and flexible fitting | - | |
|
Tom Goddard
Elaine Meng
Eric Pettersen
|
UC San Francisco | Refinement of cryoEM maps with Isolde | - | |
| Tom Goddard | UC San Francisco | Publication-quality images and movies | - | |
| Paul Adams | Lawrence Berkeley National Lab | Phenix introduction (LBNL videos are all included on this video) | Video | |
| Paul Adams | Lawrence Berkeley National Lab | Atomic models from cryo-EM data | - | |
| Pavel Afonine | Lawrence Berkeley National Lab | Structure Refinement | - | |
| Paul Adams | Lawrence Berkeley National Lab | Model validation for cryo-EM | - | |
| Pavel Afonine | Lawrence Berkeley National Lab | Structure refinement and validation practical | - | |
| Nigel Moriarty | Lawrence Berkeley National Lab | Ligands | - | |
| Greg Pintilie | Stanford University | Assessment of high resolution cryoEM features | Video | |
| Helen Berman | Rutgers University | Validation of biological structures | - | - |
| Cathy Lawson | Rutgers University | EM structure archives, validation and challenges (included with Greg Pintilie's video) | - |
2019 November 18-20, S2C2 CryoEM Image Processing Workshop: SCIPION
Other Material: agenda
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| David DeRosier | Brandeis University | General principles of cryoEM 3D reconstructions | Parts 1, 2, 3 | |
| Jose Maria Carazo | CNB-CSIC | Basic image processing for EM | PDF 1, 2 | Parts 1, 2, 3 |
| Carlos Sanchez-Sorzano | CNB-CSIC | Image processing principles | Parts 1, 2, 3 4, 5 | |
| Yiorgio Skiniotis | Stanford University | Dealing with heterogeneity in single-particle data/examples | - | |
| Greg Pintilie | Stanford University | Model building and map validation | - | - |
2019 September 11-13, S2C2 CryoEM Training for Beginners Workshop
Other Materials: agenda, Prof. Grant Jensen Videos)
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| Juergen Plitzko | Max Planck Institute | EM basics | - | |
| Yiorgio Skiniotis | Stanford University | Freezing basics | - | |
| Christopher Booth | Gatan | Camera | - | |
| Yee Ting Li | SLAC National Accelerator Lab | eLogbook and data transfer | - | - |
| Robert Glaeser | Lawrence Berkeley National Lab | Radiation damage | - | |
| Zoltan Metlagel | FEI | EPU and phase plate | - | - |
| Corey Hecksel | Stanford University | Data collection (serial EM) | - |
2019 July 10-12, S2C2 CryoEM Modeling Workshop: ChimeraX & Phenix
Other Materials: agenda, properly weighted map t20s, model validation tutorial/model optimization tutorial
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
|
Tom Goddard
Elaine Meng
Eric Pettersen
|
UC San Francisco | ChimeraX - visualization of cryoEM maps and models | - | |
| Greg Pintilie | Stanford University | Rigid body and flexible fitting | - | |
| Paul Adams | Lawrence Berkeley National Lab | Phenix introduction | - | |
| Paul Adams | Lawrence Berkeley National Lab | Automated model docking and building | - | |
| Pavel Afonine | Lawrence Berkeley National Lab | Phenix tools for cryoEM: refinement and validation | - | |
| Paul Adams | Lawrence Berkeley National Lab | Model validation for cryo-EM | - | |
| Nigel Moriarty | Lawrence Berkeley National Lab | Restraints in Phenix | - | |
| Corey Hyrc | Baylor College of Medicine | Accurate representaiton of cryoEM structures | - | |
| Greg Pintilie | Stanford University | Assessment of high resolution of cryoEM features | - | |
| Michael Robertson | Stanford University | CryoEM structure and ligand modeling | - | - |
| Cathy Lawson | Rutgers University | CryoEM archives, challenges and validation | - |
2019 March 11-13, S2C2 CryoEM Image Processing Workshop
Other Material: agenda
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| David DeRosier | Brandeis University | General principles of cryoEM image reconstruction | - | |
| Yee Ting Li | SLAC National Accelerator Lab | Data acquisition and pre-processing software logging on and computer basics | - | |
| Cornelius Gati | SLAC National Accelerator Lab | Image processing with Relion - introduction | - | - |
|
Greg Pintilie
Wah Chiu
|
Stanford University | Map visualization and validation | - | |
| Cathy Lawson | Rutgers University | Cryo-EM map challenge, map deposition and archiving | - | |
| Yiorgio Skiniotis | Stanford University | Dealing with heterogeneity in single-particle cryoEM data | - | |
| Cornelius Gati | SLAC National Accelerator Lab | Different image processing software packages | - | - |
2019 January 22-25, S2C2 CryoEM Training for Beginners Workshop
Other Materials: agenda (no recordings for this workshop)
| Speaker | Institution | Title | PPT | Video |
|---|---|---|---|---|
| Yiorgio Skiniotis | Stanford University | Cryo-specimen preparation | - | |
| Wah Chiu | Stanford University/SLAC | Radiation damage in cryoEM | - | |
| Christopher Booth | Gatan | Detection technologies for cryo-electron microscopy | - | |
| Juergen Plitzko | Max Planck Institute | TEM basics and column alignment | - | |
| David Bushnell | Stanford University/SLAC | Low dose imaging via serial EM and EPU | - | |
| Wah Chiu | Stanford University/SLAC | Image contrast theory in CryoEM | - | |
| John Spear | Thermofisher | Krios and Talos alignment | - | |
| Yee Ting Li | SLAC National Accelerator Lab | eLogbook, data collection monitoring and pre-processing | - |
