[NMRFAM enews] NMRFAM eNewsletter_ April 2018

Lai Bergeman lai.bergeman at wisc.edu
Tue Apr 10 12:18:51 CDT 2018

NMRFAM eNewsletter – April 2018

  *   June 3-8, 2018 - NMRFAM 12th Annual Structure Determination Workshop – Madison WI. Don’t miss out on this popular workshop! Limited participants. Bonus one day workshop (6/8) of “HADDOCK” by Professor Alexandre Bonvin from University of Utrecht, The Netherlands. Attached pdf for printing/ forwarding. More information - https://nmrfam.wisc.edu/introductory-workshop/

  *   May 2018 time requests: This is a reminder that April 19th 4pm CST is the deadline to have spectrometer time reserved for you for May 2018; please contact Lai Bergeman<mailto:lai.bergeman at wisc.edu> by e-mail or call 608-262-3173. You may schedule time yourself, as soon as the calendar is open by end-of-day on April 20th, by logging into Sundial and following the requests process.

  *   YouTube video tutorials and help pages for users of Sundial (creating and submitting time request) - http://www.sesame.wisc.edu/sesame_videos.html and http://www.sesame.wisc.edu/sesame_helppages.html

  *   Vosges (Bruker 600) is NOW operational.

  *   NMRFAM offers services such as:

     *   collect routine NMR spectra of small molecules, process the data with peak picking and integration, and provide their experimental results in electronic or paper format in order to advance research projects.

Users can submit their samples in 3 or 5 mm NMR tubes before 1 pm every Tuesday and Thursday. Their data will be acquired between 1 - 5 pm of the same day on a 500 MHz spectrometer optimized for 13C (no appointment necessary)

New User/Collaborator Information:
Please note that if you would like to collaborate with our facility you will need to submit an abstract providing some detail to Dave Aceti<mailto:djaceti at wisc.edu>, our coordinator, who will bring it up for review at our weekly staff meeting for approval. Please visit the NMRFAM website<http://www.nmrfam.wisc.edu/become-a-collaborator.htm> for more information.

Other NMRFAM capabilities:
Solid state probes at NMRFAM:
·         3.2mmEfree CPMAS, 4mm CPMAS and HRMAS probes - 500 MHz (Devon)
·         3.2mm Efree CPMAS and static BioProbe (PISEMA experiments) -  600 MHz III (Vosges)
·         3.2mm Efree CPMAS probe and 1.3mm ultrafast CPMAS probe- 900 MHz (Fleckvieh)

  *   LC/MS micrOTOF Q II and Bruker Nanostar SAXS (small angle X-ray scattering) instruments are now available for use and collaboration.
  *   For information about LC/MS and SAXS, please email Paulo F. Cobra<mailto:paulo at nmrfam.wisc.edu>.

  *   NMRFAM Software News:

NMRFAM-SPARKY new features:

-       Improved PINE / PINE-SPARKY 2 (ep)
-       Hydrophobic core and flexibility detection in PINE-SPARKY 2 (ep)
-       Sequence entry integration for automated tools (sq)
-       More colors available (ct, cr)
-       Move labels to peak centers (lc)
-       Dummy graph (dg) / Pine graph assigner (pp) small fix
-       Explicit buttons in the strip plot (sp / SP)
-       Completeness counter (cm)
-       Improved APES peak picker (ae)
-       Improved PONDEROSA structure calculation (c3)
-       Improved PDB use for NOESY assignment (ad)
-       FLYA peak import in read cyana tool (cy)
-       NMRPipe, NMRView, TopSpin files can be directly opened in here.
-       A new conversion script for importing NMRView to UCSF (nv2ucsf)
-       Chemical shift reference views (ir)
-       Mouse wheel (mw) and/or + / - / , / . / arrow key integration
-       Help manual updates for two-letter codes (hn / hI)

Donate to NMRFAM:
US deductible donations 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
                        Department of Biochemistry
                        433 Babcock Drive
                        Madison WI 53706
For further information, please contact Ms. Saunders, Tel: 608-265-2507 or email<mailto:slsaunders2 at wisc.edu>

Spectrometers at NMRFAM:

·         NMRFAM Spectrometers availability (Live Schedule) for current and upcoming month can be view at http://www.nmrfam.wisc.edu/Spectrometer-Live-Calendar.htm

NMRFAM instrumentation
Spectrometer status:


Cow name

Shortcut name



Bruker AV-HD 900




OK - cold 1H and13C preamps

Agilent VNS 800




OK - cold probe

Bruker AV III 750




OK - cold probe

Bruker AV III 600


600 I


OK - SampleJet

Agilent VNS 600


600 II


OK - cold probe

Bruker AV III 600


600 III


OK - cold probe

Bruker AV III 600


600 IV


OK - SampleJet (cooled)

Bruker AV III 500


500 I


OK-all cold preamp; SampleJet

Bruker AV III 500


500 II


OK - cold probe





OK - temperature control available

(a)rt - room temperature; c - cryogenic; tr - 1H{13C,15N} triple resonance; qr -1H{13C,15N,31P} quadruple resonance; multiple - multiple probes; VNS- Varian Direct Drive console; AV- BrukerAvance III console

 Below is a listing of the available software on our website that you are free to use or download and some associated publications:
2 - NMRbot
5 - PINE
6 - PINE-Sparky
8 - ADAPT-NMR Enhancer
9 - Newton
10 - PACSY
15 - NMR Structure Tools
16 – rNMR

Please visit the NMRFAM software website<http://www.nmrfam.wisc.edu/software.htm> for more information on the above listed software.

References for recent publications are:

References for recent publications are:

Cai K. Frederick RO, Tonelli M, Markley JL. ISCU(M108I) and ISCU(D39V) differ from wild type ISCU in their failure to form cysteine desulfurase complexes containing both frataxin and ferredoxin. Biochemistry. 2018 Feb PMID: 29406711

Lee, Markley JL. PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinformatics. 2017 Dec PMID:29281006

Fathi F, Brun A, Rott KH, Falco Cobra P, Tonelli M, Eghbalnia HR, Caviedes-Vidal E, Karasov WH, Markley JL. NMR-Based Identification of Metabolites in Polar and Non-Polar Extracts of Avian Liver. Metabolites. 2017 Nov PMID: 29144418

Dashti H, Westler WM, Tonelli M, Wedell JR, Markley JL, Eghbalnia HR. Spin System Modeling of Nuclear Magnetic Resonance Spectra for Applications in Metabolomics and Small Molecule Screening. Anal Chem. 2017 Nov. PMID: 29058410

Schilke BA, Ciesielski SJ, Ziegelhoffer T, Kamiya E, Tonelli M, Lee W, Cornilescu G, Hines JK, Markley JL, Craig EA.  Broadening the functionality of a J-protein/HSP70 molecular chaperone system. PLoS Genet. 2017 Oct. PMID: 29084221

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