NYSBC - New York Structural Biology Center

Simons Electron Microscopy Center

The Simons Electron Microscopy Center provides expertise and resources for understanding both molecular and cellular structures. Molecular structure determination is enabled by high-end transmission electron microscopes (TEMs), direct detection cameras, and computational support for single particle analysis. Cellular structure determination is enabled by tomographic reconstructions using the TEMs and a focused ion beam (FIB) scanning electron microscope (SEM). SEMC is supported by dues from member institutions as well as the Simons Foundation.


SEMC Renovations Krios#2

Order in the control room has been restored.

Installing the Krios#2!

Members of the lab assist in positioning the base of the new Krios#2 in its case.

Installing the Krios#3!


The Krios#3 has arrived and installation is proceeding.

Renovations to the SEMC suite are nearly complete. We expect to see Krios#2 (Cs corrector, phase plate, energy filter, K2, Falcon3) become available to users sometime before the end of January 2017. Once that occurs, we will take the opportunity to do a preventative maintenance and tip change on Krios#1, which will entail a minimum of 1-2 weeks downtime. Krios#2 (phase plate, energy filter, K2, Falcon3) is being built and should be online in the first quarter 2017.

The BioTWIN screening microscope is now up and running. The addition of this instrument allows greater throughput for optimization of vitrified samples.

Click here to view an updated renovation schedule.
Click here to learn about scheduling microscope time during the renovation period.

Request For Applications (RFA) for Krios#2 Open Beta

INSTRUMENT: Krios#2 is a 300kV Titan Krios with: 1) Cs (image) corrector, 2) Phase Plates and 3) Gatan GIF Quantum Energy Filter.

WHO IS ELIGIBLE: Open beta is designed to streamline our workflows in preparation for normal operations. Mature projects will take higher priority, however all active users from our member institutions are encouraged to apply for EM time. The minimum requirement is for users to have screened similar cryo sample conditions (including preliminary data processing) for the grids that they will be loading into the instrument.

REQUIREMENTS: Interested users should submit a proposal. Users must have: 1) registered as a user, 2) registered their project and, 3) completed a SEMC New User Orientation session (offered once a month). To apply for this orientation email EMG@NYSBC.org.

SUPPORTED WORKFLOWS: Cryo-single particle and cryo-electron tomography workflows on the Gatan K2 Summit in counting mode will be supported.


BioTWIN The FEI T12 BioTWIN screening microscope is now open for general use. As established for the JEOL1230 screening microscope, member institution users may book time on the instrument within their institutional allocation. The addition of this instrument allows greater throughput for screening and optimization of too temperature and vitrified samples.

Until users are certified to be independent on this instrument they must email EMG@NYSBC.org to request staff assistance concurrent with their reservation.

Laboratory Supplies
All SEMC users must purchase their own consumable EM supplies. Grids, grid boxes, Krios cartridges and small personal tools must be purchased prior to your lab session. We encourage you to buy these directly from the vendors. There is new information on our "To Start" page regarding how to obtain the consumable laboratory supplies that users are required provide for their projects. To learn more about it, click here. If you choose to purchase items using the PayPal method explained in the link, you must bring proof of purchase with you to the lab in order to receive your supplies.

Upcoming/Ongoing Events

SEMC Electron Microscopy Winter Course
SEMC will be offering a "reverse classroom" style EM course that will begin January 2017 and will run for 16 weeks, through May 2017. The course will be based on an online video class taught by Grant Jensen. Students will be expected to watch these lectures prior to a formal 90 minute class that will meet once per week for follow up materials and discussion.

If you wish to attend the course, please fill out an application form by December 31st, 2016. There will be a limit of 20 students and we may not be able to accept all applicants or any late comers.

For more information about the course, please click here.

To register for the course go to: https://www.surveymonkey.com/r/WinterCourse17.

May 9th, 2017
Appion Part 3 Workshop: Tomography
Leginon-Appion-Protomo: Semi-Automated Fiducial-less Tilt-Series Collection, Alignment, and Sub-Tomogram Processing

Tomography performed without fiducials has historically been an unreliable and innacurate task. At NYSBC we have developed a full workflow for fiducial-less tilt-series collection and alignment. This workshop will teach you how to perform tomography on all sample types, from single particle samples to FIB/SEM lamella for visualization in situ and for further processing with sub-tomogram alignment and averaging.

Users will learn the basics of tilt-series collection in Leginon, tilt-series alignment with Appion-Protomo, and sub-tomogram processing with Dynamo. Appion-Protomo and Dynamo will be partially hands-on.

No previous experience in tomography is required. Workshop attendees are encouraged to bring data in the form of tilt-series images, tomograms, or sub-tomograms for processing assistance.

Attendees should bring their own laptop in order to follow along during this hands-on workshop. If you are interested in attending this Appion Part 3 Workshop on May 9th from 10:00am - 4:00pm, please register at: https://www.surveymonkey.com/r/2XFVQ3T.

Recent Events

April 18, 2017
Rosetta Workshop - Frank DiMaio

On April 18th, 2017 a workshop titled "Workshop On Using Rosetta For CryoEM-Guided Protein Structure Determination" was presented by Frank DiMaio of the University of Washington in the Main Seminar Room at NYSBC. This tutorial introduced several Rosetta-based tools for structure determination guided by cryoEM density data. A general introduction to the Rosetta software suite was provided, and then specific methods for automated de novo structure determination, homology modeling, and model refinement were covered. The tutorial also described interpretation of Rosetta results and introduced several other useful tools in Rosetta to handle other experimental restraints.

April 4, 2017
NUT New User Training
New User Training is offered on the first Tuesday of every month. The morning session covers sample preparation (negative-staining and plunge freezing), and the afternoon session covers basic TEM use (loading samples and introduction to Leginon). Held this month on April 4th, the training was attended by the people in the photo above. Please email EMG@NYSBC.org to inquire about future training session dates.

March 22, 2017
SEMC Forum - Gabriella Kiss, FEI/Thermo Fisher Scientific
On March 22, Gabriella Kiss of FEI/Thermo Fisher Scientific will present a SEMC Forum titled Large-Scale Data with Nanoscale Insight, to be held in the Main Seminar Room, New York Structural Biology Center at 12:00pm

Return to the Top