The Winter-Spring 2016 EM Course

About the course

Electron microscopy in combination with image analysis is increasingly powerful in producing 3D structures of individual molecules and large macromolecular complexes that are unapproachable by other methods. This course is focused on the concepts and theories behind electron microscopy and will be taught in a reverse classroom format based on Grant Jensen’s online course (Getting Started in Cryo-EM [] from Caltech). Students will be responsible for watching these online lectures prior to class. Each week guest lecturers and SEMC staff lead discussions on the practice of solving molecular structures by electron microscopy.

The course will be held at the New York Structural Biology Center at 89 Convent Ave (133rd St) or Zoom (when appropriate).

Course Schedule

Classes in A-11 seminar room (Mon 3:30-5pm)

Jan 11 : Introduction & SEMC tour (short class) [Ed Eng & SEMC staff, NYSBC] [pdf] Jan 18 : No class – Martin Luther King
Jan 25 : Basic anatomy of the electron microscope [Christoph Wigge & Anchi Cheng, NYSBC][pdf] Feb 1 : Fourier transforms and Image Formation [Bill Rice, NYSBC][pdf] Feb 8 : Challenges in biological EM & Sample Prep [Ed Eng & Ashleigh Raczkowski, NYSBC] [pdf] Feb 15 : No class – President’s Day
Feb 22 : Tomography (part I) [David Stokes, NYU] Feb 29 : Tomography (part II: FIB-SEM ) [Christoph Wigge & Bill Rice, NYSBC] [pdf] Mar 7 : Single-particle analysis (part I) [Joachim Frank, COLU] [pdf] Mar 14 : Single-particle analysis (part II) [Amedee Des Georges & Reza Khayat, CUNY] [pdf] Mar 21 : Single-particle analysis (part III) [Yong Zi Tan, COLU/NYSBC] [pdf] Mar 28 : EMDataBank: Structure Data Archiving, Validation Challenges [Cathy Lawson, Rutgers] [pdf] Apr 4 : 2D crystallography (part II: Helical) [Hernando Sosa, AECOM][pdf] Apr 11 : 2D crystallography (part I) [Iban Ubarretxena, MSSM] [pdf] Apr 18 : Validation methods [Tom Walz, RU] [pdf] Apr 25 : Fitting Atomic Models [Willy Wriggers, Old Dominion University] [pdf] Apr 26 : Forum Presentation – Multiscale Biomolecular Modeling in 4-D @12pm [Willy Wriggers, Old Dominion University] [pdf] Apr 26 : Workshop – Multi-Scale Fitting and 4-D Modeling Workshop [Willy Wriggers, Julio Kovacs, and Manuel Wahle] [Situs_pdf][20160426_2_Workshop_TimeScapes_JK][Sculptor_pdf] May 2 : Conclusion & open discussion (short class) [SEMC staff, NYSBC] Note: The lecture slides are provided for educational purposes only. All rights are reserved by their original authors. Please contact them if you would like to use or repost their content.

Video screenings in the SEMC conference room (starts @3:30pm, optional)

Single-particle section* 
Jan 13 : Basic anatomy of the electron microscope
Jan 20 : Fourier transforms and reciprocal space
Jan 27 : Image Formation
Feb 3 : Fundamental challenges in biological EM
Feb 10 : no screening
Feb 17 : Tomography (part I)
Feb 25 : Tomography (part II)
Mar 2 : Single-particle analysis (part I)
Mar 9 : Single-particle analysis (part II)
Mar 16 : Single-particle analysis (part III)
Mar 23 : no screening
Mar 30 : 2D cystallography

Suggested class structure (1.5 hr class)

  • 30 min Introduction by guest lecturer on applying the class topic to scientific questions with focus on the nuts & bolts of the technique. Examples may be from their own research or a recent paper.
  • 15 min Coffee break/informal conversation
  • 45 min Open ended discussion covering concept check questions on the topic