[NMRFAM enews] NMRFAM eNewsletter_November 2017

Lai Bergeman lai.bergeman at wisc.edu
Wed Nov 15 11:28:51 CST 2017

NMRFAM eNewsletter – November 2017

  *   December 2017 time requests: This is a reminder that November 19th 4pm CST is the deadline to have spectrometer time reserved for you for December 2017; 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 November 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

  *   Jaulan (Agilent 600) is operational starting December 1st 2017.

  *   Vosges (Bruker 600) is not operational. It is in the process of being moved and should be available in about 1 month.

  *   Devon (500MHz II) – Starting from September 1st 2017, default probe on Devon will be 4mm CP-MAS (solid probe). If user would like to use cryoprobe, request has to be submitted on/or before the 19th of the previous month in Sundial for consideration or use Kerry (500MHz I).

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

Vosges (not operational)

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:

Wyche TP, Alvarenga RFR, Piotrowski JS, Duster MN, Warrack SR, Cornilescu G, De Wolfe TJ, Hou Y, Braun DR, Ellis GA, Simpkins SW, Nelson J, Myers CL, Steele J, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS. Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin. ACS Chem Biol. 2017 Jul. PMID 28708379

Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD. Progressive Stereo Locking (PSL) – A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and other Small Molecules. ACS Chem Biol. 2017 Jun. PMID:28617580

Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. Methods Mol Biol. 2017. PMID: 28573592

Dashti H, Westler WM, Markley JL, Eghbalnia HR. Unique identifiers for small molecules enable rigorous labeling of their atoms. Sci Data. 2017 May. PMID: 28534867

Markley JL, Westler WM. Biomolecular NMR: Past and future. Arch Biochem Biophys. 2017 May. PMID: 28495511

Chae YK, Kim SH, Markley JL. Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy. PLoS One. 2017 May. PMID:28486539

Cai K, Tonelli M, Frederick RO, Markley JL, Mitochondrial Cysteine Desulfurase and ISD11 Coexpressed in Escherichia coli Yield Complex Containing Acyl Carrier Protein. ACS Chem Biol. 2017 Mar. PMID:28233492

Cai K, Tonelli M, Frederick RO, Markley JL, Human Mitochondrial Ferredoxin 1 (FDX1) and Ferredoxin 2 (FDX2) Both Bind Cysteine Desulfurase and Donate Electrons for Iron-Sulfur Cluster Biosynthesis. Biochemistry. 2017 Jan. PMID:28001042

To Unsubscribe, go to http://lists.nmrfam.wisc.edu/mailman/options/enews

Lai Bergeman
NMRFAM Administrator
RM 171, 433 Babcock Dr.
University of Wisconsin – Madison,
Madison WI 53706
lai.bergeman at wisc.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.nmrfam.wisc.edu/pipermail/enews/attachments/20171115/4b0ec0a7/attachment.html 

More information about the enews mailing list