[NMRFAM enews] Newsletter - March 2013

Rita Hannah rhannah at wisc.edu
Thu Mar 14 11:38:11 CDT 2013


 (../wp-content/uploads/2009/09/enews_header.gif"> National Magnetic Resonance Facility at Madison March 2013 time requests: This is a reminder that March 19th @ 4pm CST, is the deadline for requesting spectrometer time in April 2013 at NMRFAM. Announcing the 2013 Protein Structure determination Workshop This year we will hold our Annual Protein Structure Determination Workshop from June 9th until June 14th. Registration and lodging information will be available on our NMRFAM(http://www.nmrfam.wisc.edu/home/workshops/) website shortly. We are also in the initial planning stages of an advanced structure determination workshop focused on structure refinement with more diverse restraints, e.g. RDCs, PREs, water refinement, etc. This workshop will be offered in 2014 and it will be better to have taken the basic protein structure determination workshop held in June. We would appreciate your input about general interest for this workshop and any other suggestions. Write to Milo Westler - milo at nmrfam.wisc.edu. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
 
 	 Below is a listing of the available software on our website that you are free to use or download and some associated publications :

 	NMRbot 
 	HIFI-NMR
 	LACS / PECAN 
 	PINE 
 	PINE-Sparky 
 	ADAPT-NMR 
 	ADAPT-NMR Enhancer
 	Newton
 	PACSY 
 	PONDERSOSA 
 	SPIDER 
 	RNA-PAIRS 
 	NMR Structure Tools
 	rNMR

 
Please visit the NMRFAM(http://www.nmrfam.wisc.edu/software/) software website for more information on the above listed software.
 
References for some of the publications are:
 
Lee, W., Bahrami, A. & Markley, J. L. (2013) ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy, Bioinformatics. 29, 4, 515-7. [PMCID:PMC23220573]
 
Clos II, L.J., Jofre, M.F., Ellinger, J.J., Westler, W.M., Markley, J.L. (2012). NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers. Metabolomics (epublished Jan. 4, 2013).
 
Bahrami, A., Clos, L. J. II, Markley, J. L., Butcher, S. E. & Eghbalnia, H. R. (2012) RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts, J. Biol. NMR. 52, 289-302. [PMCID:PMC3480180]
 
Bahrami, A., Tonelli, M., Sahu, S. C., Singarapu, K. K., Eghbalnia, H. R. & Markley, J. L. (2012) Robust, Integrated Computational Control of NMR Experiments to Achieve Optimal Assignment by ADAPT-NMR, PLoS One. 7, 233175. [PMCID:PMC3299752]
 
Lee, W., Yu, W., Kim, S. Chang, I., Lee, W. & Markley, J. L. (2012) PACSY, a relational database management system for protein structure and chemical shift analysis, J. Biomol. NMR, 154, 169-79.
 
Chylla, R. A., Hu, K., Ellinger, J. J. & Markley, J. J. (2011) Deconvolution of two-dimensional NMR spectra by fast Maximum Likelihiid Reconstruction: application to quantitative metabolomics, Anal. Chem, 83, 4871-80. [PMCID: PMC3114465]
 
Lee, W., Kim, J. H., Westler, W. M. & Markley, J. L. (2011) PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination, Bioinform. 27, 1727-8. [PMCID: PMC3106192]
 
Lewis, I. A., Schommer, S. C. & Markley, J. L. (2009) rNMR open source software for identifying and quantifying metabolites in NMR spectra, Magn. Reson. Chem., 47, (S 1), S123-S126. [PMCID: PMC2798074]
 
Lee, W., Westler, W. M., Bahrami, A., Eghbalnia, H. & Markley, J. L. (2009) PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Boinformatics. 25, 2085-7. [PMCID:PMC2723000]
 
Bahrami, A., Assadi, A. H., Markley, J. L. & Eghbalnia, H. R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol., 5(3):e1000307. [PMCID:PMC2645676]
 
Cornilescu, G. Bahrami, A. Tonelli, M., Markley, J. L. & Eghbalnia, H. R. (2007) HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections, J Biomol. NMR. 38, 341-51.
 
Wang L., Eghbalnia, H. R., Bahrami, A. & Markley, J. L. (2005) Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J Biomol. NMR, 32 (1):13-22.
 
Eghbalnia, H. R., Wang, L., Bahrami, A. Assadi, A. & Markley, J. L. (2005) Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements., J Biomol. NMR, 32 (1) 71-81.
 
Eghbalnia, H. R., Bahrami, A. Tonelli, M., Hallenga, K. & markley, J. L. (2005) High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection. J Am. Chem. Soc. 127, 12528-36.
 

 
 	 Rotvieh (700 MHz) spectrometer is unavailable and part of the facility anymore.
 	 Gelbvieh (800 MHz) spectrometer is still running on the triple resonance - room temperature probe.

 
 	 LC/MS micrOTOF Q II is now available for collaboration. Contact the facility for more information.
 	 Small Angle X-ray Scattering (SAXS):

 
>  
>  	 The Bruker Nanostar SAXS instrument is currently available by appointment only. Prior to signing up for the instrument, please email Prof. Sam Butcher (butcher at biochem.wisc.edu) and indicate "SAXS TIME" in the subject line of your email. Prof. Butcher will help you to schedule a time when someone from the facility will be available to assist you with SAXS data collection. Please note the rate for academic/collaboration use is $5/hr. and $100/hr. for commercial users.
> 
> 
 
 	 A loaner 4mm 1H{X} cpmas probe (15,000 rpm max) has been installed on the Bruker 500II (Devon) and is available by special request. This instrument has solids amplifiers and is capable of many modern solids experiments. A low-e 1H13C15N cpmas probe (24,000 rpm max) has now been installed on 500II.
 	 Devon (500 MHz II) has an updated list of probes.

 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Spectrometers at NMRFAM: 
 	 Status of spectrometers can be determined at anytime as follows: In Sundial after login, go to "Options"----->"Site Resources"----->"Spectrometers" A new set of Options open on the Sundial Board. Go to "Search"------>"By Owner". A new window pops up in the second section (Manufacturer), type/write in either "Bruker " or "Varian". A listing of the spectrometers will be displayed. Select the one of interest and check on it's status, probes available etc.
 	 NMRFAM instrumentation

 Spectrometer status: 
 
  Instrument http://www.nmrfam.wisc.edu/home/schedule-nmr-time-sundial-2/(../?page_id=500">Cow name Shortcut name Probe(a) Status
  Varian VNS 900 Fleckvieh 900 c-tr OK-cold 1H and 13C preamps
  Varian VNS 800 Gelbvieh 800 rt-tr Ok
  Bruker AV III 750 Telemark 750 c-tr Ok
  Bruker AV III 600 Dexter 600 I c-qr 1H{13C,15N,31P} OK-SampleJet
  Varian VNS 600 Jaulan 600 II c-tr OK
  Varian VNS 600 Vosges 600 III c-tr OK
  Bruker AV III 600 Kurgan 600 IV c-tr (1.7mm) OK-SampleJet(cooled)
  Bruker AV III 500 Kerry 500 I c-tr(13C/15N) OK-all cold preamp; Samplejet
  Bruker AV III 500 Devon 500 II c-tr/hrmas/BBFO/cpmas OK - swappable CP (solids capability)currently only RT probes
  Bruker DMX 400 Pisa 400 Multiple OK
  Bruker Nanostar  SAXS N/A Ok
  (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- Bruker Avance III console

 
To sign up for time: Use Sundial at
 

 
Contact Rita Hannah (rhannah at nmrfam.wisc.edu, 608-262-3173) for assistance. For scientific questions/discussions contact Milo Westler (milo at nmrfam.wisc.edu)
 
For SAXS information and scheduling contact Samuel Butcher (sebutcher at wisc.edu) <sebutcher at wisc.edu>
 
Please visit the NMRFAM(../) website for more information.
 
 
--
Rita Hannah, Ph.D.
NMRFAM
University of Wisconsin - Madison
Madison, WI - 53706
e-mail: rhannah at wisc.edu
Phone: (608) 262-3173
FAX:   (608) 262-3759


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