S2C2 |Stanford-SLAC Cryo-EM Center

Archived PDFs and VIdeos of Training Workshops and Lectures

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2021 Workshop/Lectures

2020 Workshop/Lectures

2019 Workshop/Lectures

 

 

2021 March 3-4, S2C2 CryoEM Specimen Preparation and Data Collection Workshop

Other Materials:  Agenda, Prof. Peter J. Peters Paper "Understanding the invisible hands of sample preparation for cryo-EM", Unanswered Q&A from Prof. Peter's Lecture

Speaker Institution Title PDF Video
Wednesday, March 3, 2021
Peter J. Peters (M4i) Maastricht University & CryoSol-World Understanding the invisible hands of sample preparation for cryo-EM PDF 1,2,3,4
Benjamin Bammes Direct Electron, LP Optimizing Direct Detector Design for a Range of Cryo-EM Techniques PDF 1,2,3,4
Jeffrey Lengyel Thermo Fisher The latest generation technology for Cryo-EM allowing for unparalleled scientific breakthroughs PDF 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 PDF 1,2,3
Sahil Gulati Ametek Advances in direct electron detection: getting the most out of your microscope PDF 1,2,3,4,5
Yee Ting Li SLAC National Accelerator Data Management at S2C2  PDF 1,2
Patrick Mitchell SLAC National Accelerator S2C2 data collection PDF 1
All   Final Q&A N/A 1,2,3

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2020 November 10-13,  S2C2 CryoEM CCP-EM Modeling Workshop

Other Materials: agenda, computing instructions

Speaker Institution Title PPT Video
Tuesday, November 10, 2020
Colin Palmer CCP-EM Lecture: Intro to workshop and CCP-EM PDF Video
Kevin Cowtan University of York Lecture: Automated model building with Buccaneer & Nautilus PDF Video
Kevin Cowtan University of York Tutorial: Buccaneer - 1,2,3
Paul Emsley MRC, LMB Lecture: Cryo-EM model building with modern Coot PDF Video
Paul Emsley MRC, LMB Tutorial: Coot (part 1) - Video
Wednesday, November 11, 2020
Paul Emsley MRC, LMB Tutorial: Coot (part 2) - 1,2
Maya Topf ISMB, Birkbeck Lecture: Flexible fitting of Atomic Models PDF 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 PDF Video
Thursday, November 12, 2020
Rob Nicholls MRC, LMB Lecture: Refinement against cryo-EM maps PDF 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 PDF Video
Arjen Jakobi TU Delft Tutorial: LocScale - Video
Friday, November 13, 2020
Agnel Joseph CCP-EM Lecture: Validation of cryo-EM maps and models PDF Video
Agnel Joseph CCP-EM Lecture: Model Validation - Video
Agnel Joseph CCP-EM Tutorial: Model Validation - Video
All Speakers   General Q&A Session -  

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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 - 1, 2
David Stuart Oxford University, Diamond Light Source The use of cryoEM structural information to advance SARS2-CoV-2 biology and therapy PDF 1, 2
Goran Kokic Max Planck Institute, Göttingen Structure of replicating SARS-COV-2 polymerase PDF 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 PDF Video Q&A
Stephan Wilkens SUNY Upstate Medical University Targeting Vacuolar H+-ATPase for Antiviral Therapy PDF 1, 2, 3

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2020 August 10-11, ACA 2020 Annual Meeting; WK6 Fundamentals of Single Particle CryoEM

Other Materials: agenda                           

Speaker Institution Title PPT Video
Tuesday, August 11, 2020
Mark Herzik UC San Diego Sample preparation for cryo-EM PDF 1, 2
David DeRosier Brandeis University Image contrast theory and reconstruction PDF 1, 2
Alexis Rohou Genentech Principles of image processing PDF 1, 2
Andres Leschziner UC San Diego Determining structures of challenging samples 1, 2, 3 1, 2
Wednesday, August 12, 2020
Dmitry Lyumkis Salk Institute Dealing with resolution anisotropyand considerations for high resolution structure determination PDF 1, 2, 3
Wah Chiu Stanford/SLAC Atomic modeling and the importance of validation PDF 1, 2
Ali Punjani Structural Biotechnology CryoSPARC demonstration/tutorial (see June Workshop for slides) - 1, 2, 3, 4

 

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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
Wednesday, June 10, 2020
David DeRosier Brandeis University If only... PDF 1, 2, 3
Ali Punjabi Structural Biotechnology CryoSPARC (AM) 06/10/20 User interface overview/Day 1 CryoSPARC Instructions 1, 2 1, 2, 3, 4, 5, 6
Ali Punjabi Structural Biotechnology CryoSPARC (PM) 06/10/20 PDF  7, 8, 9, 10, 11, 12
Thursday, June 11, 2020
Ali Punjabi Structural Biotechnology CryoSPARC (AM) 06/11/20 PDF 1, 2, 3, 4, 5, 6, 7, 8
Ali Punjabi Structural Biotechnology CryoSPARC (PM) 06/11/20 PDF 9, 10, 11, 12
Stephan Arulthasan Structural Biotechnology CryoSPARC architecture & management PDF Video
Ali Punjabi Structural Biotechnology CryoSPARC (PM) 06/11/20 - 13, 14, 15, 16
Friday, June 12, 2020
Greg Pintilie Stanford University CryoEM map resolution assessment, validation, visualization and segmentation PDF 1, 2, 3
Cathy Lawson Rutgers University EMDataResource: structure data archiving, validation challenges PDF 1, 2

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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 PDF 1, 2, 3, 4, 5, 6

 

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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 PDF Video
Glaeser, Robert Lawrence Berkeley National Lab Single-particle grid preparation PDF Video

 

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2020 January 15-17,  S2C2 CryoEM Modeling Workshop: ChimeraX & Phenix

Other Materials: agenda

Speaker Institution Title PPT Video
Wednesday, January 15, 2020
Tom Goddard 
Elaine Meng
Eric Pettersen
 UC San Francisco ChimeraX-Visualization of cryoEM maps and models PDF -
Greg Pintilie Stanford University Segmentation, rigid body and flexible fitting PDF -
Tom Goddard
Elaine Meng
Eric Pettersen
 UC San Francisco Refinement of cryoEM maps with Isolde PDF -
Tom Goddard UC San Francisco Publication-quality images and movies PDF -
Thursday, January 16, 2020
Paul Adams Lawrence Berkeley National Lab Phenix introduction (LBNL videos are all included on this video) PDF Video
Paul Adams Lawrence Berkeley National Lab Atomic models from cryo-EM data PDF -
Pavel Afonine Lawrence Berkeley National Lab Structure Refinement PDF -
Paul Adams Lawrence Berkeley National Lab Model validation for cryo-EM PDF -
Pavel Afonine Lawrence Berkeley National Lab Structure refinement and validation practical PDF -
Nigel Moriarty Lawrence Berkeley National Lab Ligands PDF -
Friday, January 17, 2020
Greg Pintilie Stanford University Assessment of high resolution cryoEM features PDF 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) PDF -

 

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2019 November 18-20,  S2C2 CryoEM Image Processing Workshop: SCIPION

Other Material: agenda

Speaker Institution Title PPT Video
Monday, November 18, 2019
David DeRosier Brandeis University General principles of cryoEM 3D reconstructions PDF 1, 2, 3
Jose Maria Carazo CNB-CSIC Basic image processing for EM 1, 2 1, 2, 3
Carlos Sanchez-Sorzano CNB-CSIC Image processing principles PDF 1, 2, 3, 4, 5
Tuesday, November 19, 2019
Yiorgio Skiniotis Stanford University Dealing with heterogeneity in single-particle data/examples PDF -
Wednesday, November 20, 2019
Greg Pintilie Stanford University Model building and map validation - -

 

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2019 September 11-13,  S2C2 CryoEM Training for Beginners Workshop

Other Materials: agenda, Prof. Grant Jensen Videos)

Speaker Institution Title PPT Video
Wednesday, September 11, 2019
Juergen Plitzko Max Planck Institute EM basics PDF -
Yiorgio Skiniotis Stanford University Freezing basics PDF -
Thursday, September 12, 2019
Christopher Booth Gatan Camera PDF -
Yee Ting Li SLAC National Accelerator Lab eLogbook and data transfer - -
Robert Glaeser Lawrence Berkeley National Lab Radiation damage PDF -
Friday, September 13, 2019
Zoltan Metlagel FEI EPU and phase plate - -
Corey Hecksel Stanford University Data collection (serial EM) PDF -

 

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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
Wednesday, July 10, 2019
Tom Goddard                  Elaine Meng
Eric Pettersen
 UC San Francisco ChimeraX - visualization of cryoEM maps and models PDF -
Greg Pintilie Stanford University Rigid body and flexible fitting PDF -
Thursday, July 11, 2019
Paul Adams Lawrence Berkeley National Lab (LBNL) Phenix introduction PDF -
Paul Adams LBNL Automated model docking and building PDF -
Pavel Afonine LBNL Phenix tools for cryoEM: refinement and validation PDF -
Paul Adams LBNL Model validation for cryo-EM PDF -
Nigel Moriarty LBNL Restraints in Phenix PDF -
Friday, July 12, 2019
Corey Hyrc Baylor College of Medicine Accurate representaiton of cryoEM structures PDF -
Greg Pintilie Stanford University Assessment of high resolution of cryoEM features PDF -
Michael Robertson Stanford University CryoEM structure and ligand modeling - -
Cathy Lawson Rutgers University CryoEM archives, challenges and validation PDF -

 

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2019 March 11-13,  S2C2 CryoEM Image Processing Workshop

Other Material: agenda

Speaker Institution Title PPT Video
Monday, March 11, 2019
David DeRosier Brandeis University General principles of cryoEM image reconstruction PDF -
Yee Ting Li SLAC National Accelerator Lab Data acquisition and pre-processing software logging on and computer basics PDF -
Cornelius Gati SLAC Image processing with Relion - introduction - -
Tuesday, March 12, 2019
Cornelius Gati SLAC Practical 2 & 3 N/A N/A
Wednesday, March 13, 2019
Greg Pintilie
Wah Chiu
 Stanford University Map visualization and validation PDF -
Cathy Lawson Rutgers University Cryo-EM map challenge, map deposition and archiving PDF -
Yiorgio Skiniotis  Stanford University Dealing with heterogeneity in single-particle cryoEM data PDF -
Cornelius Gati SLAC Different image processing software packages - -

 

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2019 January 22-25,  S2C2 CryoEM Training for Beginners Workshop

Other Materials: agenda  (no recordings for this workshop)

Speaker Institution Title PPT Video
Tuesday, January 22, 2019
Yiorgio Skiniotis Stanford University Cryo-specimen preparation PDF -
Wah Chiu Stanford/SLAC Radiation damage in cryoEM PDF -
Christopher Booth Gatan Detection technologies for cryo-electron microscopy PDF -
Wednesday, January 23, 2019
Juergen Plitzko Max Planck Institute TEM basics and column alignment PDF -
David Bushnell Stanford/SLAC Low dose imaging via serial EM and EPU PDF -
Wah Chiu Stanford/SLAC Image contrast theory in CryoEM PDF -
Thursday, January 24, 2019
John Spear Thermofisher Krios and Talos alignment PDF -
Yee Ting Li SLAC eLogbook, data collection monitoring and pre-processing PDF -

 

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