NYSBC - New York Structural Biology Center


Quick Start Guides:

SEMC Training Manual
Click here to view/print the SEMC Training Manual
Appion Guide
Click here to view/print the SEMC Appion Manual
Leginon Guide
Click here to view/print the SEMC Leginon Manual

Papers to Review

  1. A Primer to Single-Particle Cryo-Electron Microscopy.

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  2. Structural analysis of macromolecular assemblies by electron microscopy.

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  3. High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles.

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  4. Structural analysis of supramolecular assemblies by cryo-electron tomography.

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  5. Visualizing proteins and macromolecular complexes by negative stain EM: from grid preparation to image acquisition.

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  6. Visualizing molecular machines in action: Single-particle analysis with structural variability.

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Online Video Courses

  1. NRAMM Workshops: http://nramm.nysbc.org/workshops/

  2. MRC Lectures: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course

    With the recent advances in cryo-EM structure determination, we find that an ever increasing number of people want to learn about it. To aid those new to the field, together with Lori Passmore and Paula daFonseca, we organized a course at LMB that covers the theoretical basis of modern cryo-EM structure determination. The slides and professionally edited videos of all ten lectures in this course may be downloaded for free from the above link.

  3. Jensen Lab Lectures: http://cryo-em-course.caltech.edu/
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Automation Tools

  1. Automation in single-particle electron microscopy connecting the pieces.

    Throughout the history of single-particle electron microscopy (EM), automated technologies have seen varying degrees of emphasis and development, usually depending upon the contemporary demands of the field. We are currently faced with increasingly sophisticated devices for specimen preparation, vast increases in the size of collected data sets, comprehensive algorithms for image processing, sophisticated tools for quality assessment, and an influx of interested scientists from outside the field who might lack the skills of experienced microscopists. This situation places automated techniques in high demand. In this chapter, we provide a generic definition of and discuss some of the most important advances in automated approaches to specimen preparation, grid handling, robotic screening, microscope calibrations, data acquisition, image processing, and computational infrastructure. Each section describes the general problem and then provides examples of how that problem has been addressed through automation, highlighting available processing packages, and sometimes describing the particular approach at the National Resource for Automated Molecular Microscopy (NRAMM). We contrast the more familiar manual procedures with automated approaches, emphasizing breakthroughs as well as current limitations. Finally, we speculate on future directions and improvements in automated technologies. Our overall goal is to present automation as more than simply a tool to save time. Rather, we aim to illustrate that automation is a comprehensive and versatile strategy that can deliver biological information on an unprecedented scale beyond the scope available with classical manual approaches.

  2. Leginon: http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage

  3. Appion: http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home

  4. An Introduction to Appion: https://www.youtube.com/watch?v=Wlxt_4yJKgA

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