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.


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.

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.


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.

February 23, 2017
Appion Workshop: Advanced Techniques - Going from Appion to RELION 2 and FREALIGN
A one-day master class will be held February 23rd from 10:00AM to 4:00PM for experienced Appion users interested in using RELION2 and FREALIGN for 3D refinements. The focus of this workshop will be how to take advantage of tools within Appion for efficient single particle analysis concurrent with Leginon data collection. A real-time demonstration will be given using our GPU workstations including a brief overview of the RELION2 and FREALIGN interfaces. The workshop limited to 10 attendees. If you are interested in attending this Appion Workshop, please register at: https://www.surveymonkey.com/r/NYHZ7BC.

March, 2017
Appion Part 2 Workshop
A one-day Appion Workshop will be held in March (date TBD). This Appion Part 2 Workshop is a follow-on to the Part 1 workshop and focuses on 3D initial models and refinement. If you are interested in attending the Appion Part 2 Workshop, please register at: https://www.surveymonkey.com/r/257V9WN.

February 6-7, 2017
Workshop on Management of Large CryoEM Facilities
App1 Here are the attendees of the Workshop on Management of Large CryoEM Facilities, held on February 6th and 7th. A major goal of the workshop was to discuss best practices for managing CryoEM facilities. Topics discussed included sample handling, instrument management, computational environments, training, user management and workflow. The workshop will be posted on the SEMC/NRAMM Youtube channel https://www.youtube.com/c/nrammsemc in the next few days.

January 10, 2017
Appion Part 1 Workshop
App1 A one-day Appion Workshop was held on Tuesday, January 10th from 10:00AM to 4:00PM. The Appion Part 1 Workshop provides hands-on training for the Appion single-particle data processing workflow. Appion is a "pipeline" for processing and analysis of EM images and is integrated with Leginon data acquisition. Topics include analyzing the quality of your data collection, correcting the CTF, generating and cleaning up stacks, and generating 2D class averages. An Appion Part 2 Workshop will be offered in the following month to provide training for making initial models and doing 3D reconstructions. If you are interested in learning when the next Appion Part 1 Workshop will be held, please e-mail EMG@NYSBC.org.

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