Leginon Workshop: Krios Data Collection at SEMC (How to get the most out of your Krios session)
November 8, 2018
10am-3pm – SEMC Conference Room
Leginon is a system designed for automated collection of images from a transmission electron microscope. This workshop is intended for active Krios users to more effectively and efficiently use the platform for high resolution single particle data collection. We will also show the full sample handling process at SEMC from grid drop off to loading.
Register here:I’m interested in Krios Data Collection!
Appion Part 3: Cryo Electron Tomography
December 6, 2018
10am-3pm- SEMC Conference Room
Tilt-series alignment is commonly performed by tracking fiducials in order to recover the three-dimensional structure and orientation of specimen in cryo-electron tomography, negative stain tomography, and tomography on plastic sections. However this approach is sometimes fraught with difficulty due to fiducial movement, fiducial aggregation, or the lack of fiducials in specimen such as FIB/SEM lamella. In this workshop users will gain hands-on experience with a semi-automated implementation of Protomo into Appion.
If you are interested in attending, please register at: I’m interested in Appion Pt. 3!
2019 SEMC Winter-Spring EM Course
January-May 2018 (see dates and times below)
New York Structural Biology Center at 89 Convent Ave (133rd St).
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.
For more information, please see: I’m interested in the Winter Course
Preliminary Course Schedule
Classes in A-11 seminar room (Mondays 3:30-5pm and select Wednesdays 3:30-5pm)
EM fundamentals section (month of January)
Jan 7 : Introduction & SEMC tour [Ed Eng, NYSBC]
Jan 9 : Basic anatomy of the electron microscope [Anchi Cheng, NYSBC]
Jan 14 : Challenges in biological EM & Sample Prep and practical [SEMC staff, NYSBC]
Jan 16 : Support films and practical [SEMC staff, NYSBC]
Jan 21 : No class – Martin Luther King Jr. Holiday
Jan 23 : Fourier transforms and Image Formation [Lorenzo Finci, NYSBC]
Jan 28 : Tomography (part I: Intro and overview of ET) [Wei Dai, Rutgers]
Feb 4 : Tomography (part II: FIB-SEM) [Bill Rice, NYSBC]
Feb 11 : Tomography (part III: Cryo-Applications & Sub-tomogram averaging) [Alex Noble, NYSBC]
Feb 18 : No class – President’s Day
Single particle section
Feb 25 : Single-particle analysis (part I: Intro and overview of SPA) [Joachim Frank, COLU]
Mar 4 : Single-particle analysis (part II: Data Analysis and reconstruction workflow [Reza Khayat, Amedee des Georges CUNY]
Mar 11 : Single-particle analysis (part III: Reconstruction workflow (cont), and Interpretation and Limitations) [Rich Hite, MSKCC]
EM crystallography section
Mar 18 : MicroED and 2D crystallography intro [Bill Rice, NYSBC]
Mar 25 : Helical (part I: Intro and overview of helical) [Greg Alushin, RU]
Apr 1 : Helical (part II: Helical cont) [Hernando Sosa, AECOM]
EM challenges and new frontiers
Apr 8 : Validation methods [Tom Walz, RU]
Apr 15 : EMDataBank: Structure Data Archiving, Validation Challenges [Cathy Lawson, Rutgers]
Apr 22 : Moderate resolution interpretation [Gira Bhabha, NYU]
Apr 29 : Fitting Atomic Models [Oli Clarke, COLU]
May 1 : Conclusion & open discussion (short class)
Lecture slides from the 2016 course may be found here, 2017 course may be found here and 2018 course may be found here. 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.
Practicals/Journal club in the SEMC conference room (starts @3:30pm)
EM challenges and new frontiers
For researchers taking the course for credit, the final score will be tabulated as follows:
Practical Worksheet 10% x 4
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 recent papers.
15 min Coffee break/informal conversation
45 min Open ended discussion on the topic. Conversation starters may come from concept check questions on the topic or presentation on newer developments in the field.