2017 NMRFAM Introductory Structure Determination Workshop

Sunday, June 4, 2017 - Friday June 9, 2017

Location. Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544 Google Map | Campus Map

Scope. This introductory, hands-on workshop will cover the basic steps involved in solving a protein structure by NMR and give participants an opportunity to practice these steps in hands-on sessions led by the NMRFAM staff. Using triple-resonance NMR data collected at NMRFAM on labeled ubiquitin, the staff will guide participants through the following steps of protein structure determination.

1 - Description of experimental data
2 - Introduction to NMRFAM-Sparky and peak picking
3 - Backbone assignment
4 - Sidechain assignment
5 - TOCSY and NOE assignments
6 - Automated assignments using PINE
7 - Three-dimensional structure determination and refinement
8 - Structure validation
9 - Deposition of the data to BioMagResBank

This workshop is intended to give participants a broad overview of the process of solving a protein structure by NMR so they can begin their own projects. Participants will bring their own laptop computers and will receive an NMRFAM software suite containing a complete set of tools for biomolecular NMR studies that they can take home. This software provides easy access to external servers, websites, and video tutorials. Nevertheless, owing to the complexity of the process, participants may require further assistance to solve a structure on their own. Participants are invited to contact NMRFAM staff following the workshop with any questions or problems.

Format. Each section will begin with a short lecture / demonstration followed by a hands-on session in which participants will be given time to perform each step of protein structure determination using data provided by NMRFAM. The staff will be available during workshop sessions to assist participants and answer questions.

Schedule and Important Dates

Thursday, May 18, 2017 - Last day to obtain block housing at Dejope Residence hall (see Lodging)

Thursday, June 1, 2017 - Last day to obtain block housing at Best Western Inn Towner (see Lodging)

Monday, May 29, 2017 - Last day to register for the workshop

Sunday, June 4, 2017 (2:30pm) - Workshop Opening Reception/Computer Set-up (ATTENDANCE REQUIRED)

Monday to Thursday, June 5-8, 2017 - Full days of workshop

Friday, June 9th, 2017 - 3:30pm - Workshop ends

Participant Requirements. Workshop participants are not expected to have prior experience with basic steps of NMR protein structure determination. The workshop will cover the entire process and each session will build upon the previous sessions. Participants will be given the data necessary to complete each session. For example, processed data will be provided for the peak-picking session, and fully peak-picked data will be provided for the backbone and side-chain assignment sessions.

This year's workshop will utilize NMRFAM’s new Integrative NMR package, which makes biomolecular NMR spectroscopy much more accessible by integrating software tools so that they interact efficiently in ways that support automation, result validation, and data visualization. Also included are links to web services, databases, and video tutorials. Participants will receive these tools pre-installed in a virtual machine that they will load onto their laptop computer (see below). Integrative NMR includes NMRFAM-SPARKY (visual analysis of spectra and chemical structures), PyMOL (visualization of 3D molecular structures), PINE (protein chemical shift assignment), PECAN (secondary structure determination from chemical shifts), RNA-PAIRS (RNA assignment), and PONDEROSA-C/S (NMR-structure determination utilizing XPLOR-NIH/Ponderosa).

Integrative NMR utilizes a virtual machine (VM), an emulation of a particular computer system that can be installed and run on all flavors of other operating systems. We use a VM that runs the Linux operating system Ubuntu 16.04 with the MATE desktop. To run this on your computer, you will need to install a VM VirtualBox (Oracle), which is freely available at www.virtualbox.org. Oracle VM VirtualBox is a virtualization software package for x86 and AM64/Intel64-based computers. Supported host operating systems include Mac OS X, Windows XP, Windows Vista, Windows 7 and Windows 8, among others. In order to install VirtualBox, you MUST have administrative privileges on your computer. It is recommended that the computer have 4 GB of memory. The memory and bit size are not strict requirements, but the speed will suffer and make the workshop rather painful. The computer should have ~10 GB of free disk space.

Registration. The fee for the workshop is $550 and includes all materials necessary to participate in the workshop, as well as the opening reception, barbecue dinner, and morning and afternoon refreshments. The registration fee DOES NOT include your lodging / housing or parking costs (see below for more information). Your registration payment of EXACTLY $550 must be sent in along with your registration form. Registration Form.

Parking. To arrange for parking at NMRFAM during the workshop, or at any campus lodging option, such as Dejope Residence Hall, visit UW-Madison's Transportation Services website, email them, or call them at 608-262-5576 during normal business hours between 8:30 a.m.-4:15p.m. CST, Monday through Friday.

Workshop Lodging OptionsLodging. Several options are available for lodging on-campus or off-campus and we have reserved blocks of rooms at two venues. For details, see NMRFAM Workshop Lodging Options.

If you have any questions about the workshop and how to register, contact Lai Bergeman or 608‑262‑3173.

We hope you can participate in this popular workshop and become an NMRFAM user!

Become an NMRFAM User
Contacts | Map | Policy
Instrumentation w/Rates
Pulse Programs
Remote Access to NMRFAM
Spectrometer Live Calendar
Sundial (Request NMR Time)
Software Tools
e-News Sign-Up

Biochemistry 800 - Practical Nuclear Magnetic Resonance Theory 

Biochemistry 801 - Biochemical Applications of Nuclear Magnetic Resonance 

"The Future of NMR-Based Metabolomics, Current Opinion in Biotechnology (2017), pp. 34-40

Documents on the use of the Bruker-Axs Nanostar,SAXS instrument and analysis of SAXS data are now available.

NMRFAM-SPARKY Distribution - the popular NMR analysis program SPARKY recompiled (including updated python and Tcl/Tk) with incorporation of PINE-Sparky, enhancements to import/export to the structural analysis program CYANA, and other useful python extensions.

ADAPT-NMR Enhancer: Complete Package for Reduced Dimensionality in Protein NMR Spectroscopy

RNA-PAIRS: RNA Probabilistic Assignment of Imino Resonance Shifts

PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis 


Donate to NMRFAM. US tax-deductible donation can be made to NMRFAM
Please write check payable to "UW Foundation, Account 112152802"  
And mail to: 
Attn: Sarah Lynn Traver Saunders
Associate Administrative Program Specialist 
University of Wisconsin-Madison 
433 Babcock Drive 
Madison, WI 53706 
Tel: 608-265-2507 or email 


1st: Lai Bergeman 
Rm 171; Phone 262-3173

2nd: Milo Westler
Rm B160; Phone 263-9599

3rd: Paulo F. Cobra
Rm B224; Phone 265-3303

4th: Marco Tonelli
Rm B160; Phone 263-9493

5th: John Markley
Rm 171A; Phone 263-9349

We welcome your questions and feedback!

NMRFAM Established 1987