[NMRFAM enews] NMRFAM eNewsletter_September 2019

Lai Bergeman lai.bergeman at wisc.edu
Fri Sep 13 11:10:36 CDT 2019

NMRFAM eNewsletter – September 2019

  *   October 2019 time requests: This is a reminder that September 19th 2pm CST is the deadline to have spectrometer time reserved for you for October 2019; 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 September 20th, by logging into Sundial and following the requests process.

  *   Chicago Area NMR Discussion Group (CANMRDG) will be held on Saturday, November 2nd 2019 in Madison, WI. An added feature for this year’s meeting is a workshop on NMRbox on Friday, November 1st, 2019. Registration and more information – https://www.chem.purdue.edu/canmrdg/. Register today!

  *   Devon (500MHz II) – Default probe on Devon will be 4mm CP-MAS (solid probe).

  *   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

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).
  *   Please email Paulo F. Cobra<mailto:paulofcobra at gmail.com> when you drop off your samples.
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 Lai Bergeman<mailto:lai.bergeman.wisc.edu>, coordinator, who will bring it up for review at our weekly staff meeting for approval. Please visit the NMRFAM website<https://nmrfam.wisc.edu/become-a-collaborator/> 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)

  *   Bruker Nanostar SAXS (small angle X-ray scattering) instrument is operational.
  *   For more information about SAXS, please email Paulo F. Cobra<mailto:paulo at nmrfam.wisc.edu>.
NMRFAM Software News:
GISSMO enables the efficient calculation and refinement of spin system matrices (chemical shift and coupling constants) against experimental 1D-1H NMR spectra of small molecules. The library of compounds parameterized by GISSMO contains more than 1286 compounds, including many key mammalian metabolites and a library of drug-like molecular fragments used in ligand screening.
Unique and reproducible molecule and atom identifiers are required to ensure the correct cross-referencing of properties associated with compounds archived in databases. The best approach to this requirement is the International Chemical Identifier (InChI). ALATIS is an adaptation of InChI that provides unique and reproducible atom numbering for all atoms including hydrogens.
NMRFAM-SPARKY new features:

     *   More colors available (ct, cr)
     *   Move labels to peak centers (lc)
     *   Help manual updates for two-letter codes (hn / hI)
     *   NMRPipe, NMRView, TopSpin files can be directly opened in here.
     *   A new conversion script for importing NMRView to UCSF (nv2ucsf)
     *   Mouse wheel (mw, Win excl.) and/or + - , . arrow key integration
     *   Contour shortcuts added (shift ) ; ' [ ]
     *   Very large data support (>10GB) for 64bits (Linux 64 / Mac)
     *   Triple strip plots and their enhancements (sp / SP / Sp)
     *   Completeness counter (cm)
     *   Chemical shift reference views and versatile assigner (ir / va)
     *   Advanced selection tool (SE) from Rienstra group
     *   PluqIn-Sparky (pq) inspired from Rienstra's plugin and PINE-SPARKY.2
     *   Transfer and simulate (ta) also supports aromatic experiments
     *   Improved APES peak picker (ae)- full automation to I-PINE/PONDEROSA
     *   I-PINE/PINE-SPARKY.2 (ep) also supports some 4D experiments
     *   Improved PONDEROSA structure calculation plugin (c3)
     *   To share the thoughts, visit Sparky user forum (Type SF)
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:

o   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:
Markley JL, Dashti H, Wedell JR, Westler WM, Eghbalnia HR. Tools for Enhanced NMR-Based Metabolomics Analysis<https://link.springer.com/protocol/10.1007%2F978-1-4939-9690-2_23>. Methods Mol Biol. 2019. PMID:31463858
Lee W, Bahrami A. Dashti Ht, Eghbalnia HR, Tonelli M, Westler WM, Markley JL. I-PINE web server: an integrative probabilistic NMR assignment system for proteins<https://link.springer.com/article/10.1007%2Fs10858-019-00255-3>. J Biomol NMR. 2019 May. PMCID:PMC6579641
Tsvetkov P, Detappe A, Cai K, Keys HR, Brune Z, Ying W, Thiru P, Reidy M, Jugener G, Rossen J, Kocak M, Kory N, Tsherniak A, Santagata S, Whitesell L, Ghobrial IM, Markley JL, Lindquist S, Golub TR. Mitochondrial metabolism promotes adaptation to proteotoxic stress<https://www.nature.com/articles/s41589-019-0291-9> . Nat Chem Biol. 2019 Jul. PMID:31133756
Dashti H, Wedell JR, Westler WM, Markley JL, Eghbalnia HR. Automated evaluation of consistency within the PubChem Compound database<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380220/>. Sci Data. 2019 Feb. PMCID:PMC6380220
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-- Milo
National Magnetic Resonance Facility at Madison
      An NIH-Supported Resource Center

W. Milo Westler, Ph.D.

NMRFAM Director
Distinguished Scientist
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
DeLuca Biochemistry Laboratories
433 Babcock Drive
Rm B160D
Madison, WI USA 53706-1544
EMAIL: milo at nmrfam.wisc.edu<mailto:milo at nmrfam.wisc.edu>
PHONE: (608)-263-9599
FAX: (608)-263-1722
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