• NMRFAM-Spectrometers

NMRFAM Policy Statement


Overview. NMRFAM supports applications of nuclear magnetic resonance (NMR) spectroscopy to biochemical and biological systems, in particular to structure-studies of biomacromolecules. The facility contains high-field, state-of-the-art NMR spectrometers for data collection and computers for processing and analyzing NMR data. Nine modern multinuclear NMR spectrometers with field strengths between 400 MHz and 900 MHz are equipped for the most demanding multidimensional, multinuclear spectroscopic applications. Cryogenically cooled probes are installed on five of the instruments. Both Bruker and Varian spectrometers are available. Projects focus on structural determinations and development of methods. NMRFAM staff members carry out core research projects and make available to service and collaborative users the techniques and technology developed through these projects. NMRFAM staff are experts in various fields of NMR experimentation and may collaborate with users who have projects of mutual interest.

Research Emphasis. The research focus of the facility is the important areas of: (1) fast data collection and automated data analysis, (2) technology for larger proteins and complexes, (3) investigations of metal-containing (paramagnetic) proteins, (4) dynamics of macromolecules, and (5) structure-function investigation of RNA molecules and their complexes with metal ions and proteins. By pursuing its innovative research technology development activities and by applying them to collaborative projects of biological importance, NMRFAM strives to be a model for demonstrating the future capabilities of the biomolecular NMR field. NMRFAM offers start-to-finish support for biomedical NMR investigations. As needed, NMRFAM will lend support to one or more of the following steps: (1) strategy evaluation, (2) sample preparation, (3) feasibility studies, (4) data collection, and (5) data analysis and structure determination. Our aim is to facilitate the efficient pursuit of new knowledge by providing researchers with resources matched to their particular needs. NMRFAM provides young investigators and experienced spectroscopists access to state-of-the-art instrumentation with support for multiple modes of data collection.

Protocols, Pulse Sequences, and Software Tools. Our aim is to develop and disseminate advanced approaches to experiment design and data analysis that cover all steps in a biomolecular NMR investigation, from cloning through data deposition. With the goal of broadening the scope of its scientific activities, NMRFAM hosts distinguished visiting scientists working in areas related to its research technology development projects. As a means for training its user base and for disseminating its novel technology, NMRFAM conducts workshops and group training sessions.

Data Storage, Analysis, and Display. Computers are available at NMRFAM for NMR data processing, analysis, structure calculations, and quantum mechanics. Nine rack mounted supermicro servers: two 3 GHz dual core Pentium D that are assigned as the entry points through the firewall to the facility network via the secure shell, ssh; Two 5 TB RAID 10 (total space 24 TB) system for home directories and working space data storage; two 2 GHz 4Xquad core AMD Opteron (Barcelona) compute servers with 32 GB memory and 1 TB RAID 1 system; one 2 GHz 4X6 core Xeon compute server with 48 GB memory and 1 TB RAID 1 system; two 1.5 TB RAID 5 systems for backup of spectrometer data (currently this function is carried out by 2 DAT tape juke boxes); a 2 X dual core AMD system that acts the compute server for the PINE web server; and a 2 X quad core AMD system for administrative purposes. All of these computers run the CentOS or Fedora Linux operating system. Other NMRFAM computers include two SGI Altix 3300 compute servers each with 12 Intel 1.3 GHz Itanium 2 processors. Each machine has a total of 27.5 GB of main memory. Both systems are equipped with a 1 TB Fiber RAID for data storage. These systems are running SGI Advanced Linux server OS.

Four Dell 3×0 workstations running RedHat Linux serve as Varian spectrometer console hosts. Five SGI O2 systems running IRIX 6.5 serve as Bruker spectrometer console hosts. One Dell 390 running spectrometer softare serves as an offline data station. 16 O2s (R5K, R10K, R12K) and 5 Octanes (R10K with SI or SSI graphics). These machines run IRIX 6.5. Two Sun Microsystems workstations running Solaris 8 or 9. Numerous other diverse species of computers are part of the NMRFAM network.

Networking. The NMRFAM network infrastructure consists of 10/100/1000 Gb or 10/100 Mb Hewlett-Packard network switches and a 11 Mb wireless access point in the computer suite (Biochemistry Room B160). A 1 GB stwich links the Supermicro servers. Users can archive data on CD or DVD. Data can be transferred over the network to and from the facility.

User Laboratory. A small laboratory is available to outside users of the facility. Its equipment includes a pH meter, NMR tube centrifuge, lyophilizer, refrigerator and freezer, fume hood, and balance. Desks and workstations are available for short-term visitors, and an office is available for longer-term visitors.

Access. Proprietary use of the facility equipment is permitted, but charged at industry rate. An agreement will be in place before an industrial user starts a project. User fees for NMRFAM are posted here. Projects of a proprietary nature must be disclosed to NMRFAM prior to the first use of NMRFAM equipment, and NMRFAM reserves the right to decline research of this nature. Proprietary projects are charged at the industry rate, and publication of the result is not required.

Technical Assistance and Training. Persons who make extensive or non-routine use of the facility are encouraged to gain hands-on experience with the instruments so they can obtain and process data independently; members of the facility staff train these major users in the operation of the spectrometers. Spectrometers can be operated remotely over the web by qualified operators. Training can be requested by prior arrangement with NMRFAM staff members. New users who have signed up for data collection time can arrange for up to eight hours of training (usually over multiple sessions) free of additional charge over the normal spectrometer user fees. Additional training is available at the normal operated-assisted rates.

Collaboration. NMRFAM instrumentation may be used independently and with “no strings attached.” However, a project that will make extensive use of facility staff or will require development of new experimental protocols should be arranged as formal collaborations backed up by letters of collaboration; co-authorship of publications is by mutual consent with knowledge and agreement of all authors prior to submission of manuscripts.

Routine Spectroscopy Service. Routine spectra can be obtained and analyzed by facility staff on a service basis. Staff members are available for consultation on experiment design and training in data acquisition and processing. To request service, complete the NMRFAM Service Spectroscopy / Service Time Request Form and bring the completed form when samples are submitted.

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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