[NMRFAM enews] April 2013 - Newsletter

Rita Hannah rhannah at wisc.edu
Fri Apr 12 10:02:21 CDT 2013

NMRFAM e-news

National Magnetic Resonance Facility at Madison

May 2013 time requests:

This is a reminder that April 19th @ 4pm CST, is the deadline for requesting
spectrometer time in May 2013 at NMRFAM.

Register for 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 is now
available on our NMRFAM <http://www.nmrfam.wisc.edu/home/workshops/>

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 
*	PINE-Sparky 
*	ADAPT-NMR Enhancer
*	Newton
*	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,

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.

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:

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.

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,


*	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:


Cow name <http://www.nmrfam.wisc.edu/?page_id=500> 

Shortcut name



Varian VNS 900




OK-cold 1H and 13C preamps

Varian VNS 800





Bruker AV III 750





Bruker AV III 600


600 I

c-qr 1H{13C,15N,31P}


Varian VNS 600


600 II



Varian VNS 600


600 III



Bruker AV III 600


600 IV

c-tr (1.7mm)


Bruker AV III 500


500 I


OK-all cold preamp; Samplejet

Bruker AV III 500


500 II


OK - swappable CP (solids capability)currently only RT probes

Bruker DMX 400





Bruker Nanostar




(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) <mailto:sebutcher at wisc.edu> 

Please visit the NMRFAM <http://www.nmrfam.wisc.edu/>  website for more



Rita Hannah, Ph.D.


University of Wisconsin - Madison

Madison, WI - 53706

e-mail:  <mailto:rhannah at nmrfam.wisc.edu> rhannah at nmrfam.wisc.edu

Phone; (608) 262-3173

FAX: (608) 262-3759


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