[NMRFAM enews] Newsletter - February 2013

Rita Hannah rhannah at wisc.edu
Wed Feb 20 14:39:19 CST 2013


My apologies for the delay even though it was available online from
02/12/2013

Rita

 <http://www.nmrfam.wisc.edu/wp-content/uploads/2009/09/enews_header.gif>
NMRFAM e-news

National Magnetic Resonance Facility at Madison

February 2013 time requests:

This is a reminder that February 19th @ 4pm CST, is the deadline for
requesting spectrometer time in March 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. Look for registration and lodging information
in future newsletters and next month on our website.

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. 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-ENHANCER 
*	Newton 
*	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:

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 (submitted with
revisions).

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]

Woonghee, L., 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

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

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

http://www.nmrfam.wisc.edu/home/schedule-nmr-time-sundial-2/

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 contact Samuel Butcher (sebutcher at wisc.edu)
<mailto:sebutcher at wisc.edu> 

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

 

 

Rita Hannah, Ph.D.

NMRFAM

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

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.nmrfam.wisc.edu/pipermail/enews/attachments/20130220/e72185ef/attachment.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.gif
Type: image/gif
Size: 1556 bytes
Desc: not available
Url : http://lists.nmrfam.wisc.edu/pipermail/enews/attachments/20130220/e72185ef/attachment.gif 


More information about the enews mailing list