BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > NMR community > News from NMR blogs
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 08-21-2010, 08:15 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Fast 90 Degree Pulse Determination

Fast 90 Degree Pulse Determination

Almost all NMR measurements rely on the correct calibration of 90° pulses. This is traditionally done by collecting a series of spectra as a function of pulse duration, finding a null for the 180° or 360° pulse and calculating the 90° pulse by simple division by 2 or 4 in the case of the 180° and 360° nulls, respectively. This determination, although trivial, can be very time consuming. Wu and Otting* have presented a much faster method of determining a 90° pulse based on measuring the nutation of a magnetization vector directly. Continuous nutation is depicted in the figure below. Here, the sample is subjected to continuous irradiation about the x axis. While being irradiated, the magnetization vector rotates in the z-y plane at a nutation frequency proportional to the pulse power. The magnetization on the -y axis is defined by a sine function. Fourier transformation of this magnetization gives an antiphase doublet centered at zero whose splitting ?? is twice the nutation frequency. The reciprocal of the nutation frequency is the time it takes the magnetization vector to rotate one complete cycle in the z-y plane and therefore the time it takes to rotate by one quarter of a cycle (i.e. the 90° pulse duration) is defined as 1/(2 ??). The problem with continuous irradiation is that the sample must be irradiated at the same time magnetization is being detected. To eliminate this problem, a scheme similar to homonuclear decoupling is used where the radiation is turned off long enough to sample a data point. This is depicted in the figure below.Here each dwell period is divided up into a period for irradiation and a period for detection. The duty cycle for the irradiation is the fraction of time for which the sample is being irradiated. The magnetization is sampled when the power is off. As in the case for continuous irradiation, the magnetization vector still rotates in the z-y plane however, the rotation is slower as it is scaled according to the duty cycle. The duration of the 90° pulse is d/(2 ??), where d is the duty cycle for irradiation. An example of this is shown in the figure below. The nutation spectrum was measured for HDO using a duty cycle, d = 0.10 and a power level of 12 dB (Bruker). Since the response of the amplifiers is linear, the 90° pulses at higher power levels can be calculated. Each decrease by 6 dB cuts the duration of the 90° pulse in half. In this case the 90° pulse at 0 dB was calculated to be 10.93 µsec at 0 dB based on the measured 90° pulse of 43.71 µsec at 12 dB. This pulse agrees to within a couple of percent of that measured by the more traditional method however, the measurement took only a few seconds. You can use a program called "pulsecal" on newer Bruker spectrometers to do this in complete automation.

--


* Peter S.C. Wu and Gottfried Otting J. Mag. Res. 176, 115 (2005).






Source: University of Ottawa NMR Facility Blog
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[U. of Ottawa NMR Facility Blog] Probe Tuning and 90 Degree Pulses
Probe Tuning and 90 Degree Pulses In order to get meaningful results from multiple-pulse NMR pulse sequences, it is essential that the 90° and 180° pulses are calibrated at the power levels used in the sequences (see this post for example). The calibrations are usually done on a standard sample in a well tuned and matched probe. The calibrations are typically stored in a file which is called up when setting up particular NMR experiments. It is important to know that these calibrations are correct for the particular sample of interest only when the probe is well tuned and matched. For...
nmrlearner News from NMR blogs 0 09-16-2011 10:02 PM
[NMRwiki tweet] nmrwiki: How to learn #nmr pulse programming?http://qa.nmrwiki.org/question/259/learning-pulse-programming
nmrwiki: How to learn #nmr pulse programming?http://qa.nmrwiki.org/question/259/learning-pulse-programming nmrwiki: How to learn #nmr pulse programming?http://qa.nmrwiki.org/question/259/learning-pulse-programming Source: NMRWiki tweets
nmrlearner Twitter NMR 0 05-13-2011 07:49 PM
Fast methionine-based solution structure determination of calcium-calmodulin complexes
Fast methionine-based solution structure determination of calcium-calmodulin complexes Abstract Here we present a novel NMR method for the structure determination of calcium-calmodulin (Ca2+-CaM)-peptide complexes from a limited set of experimental restraints. A comparison of solved CaM-peptide structures reveals invariability in CaMâ??s backbone conformation and a structural plasticity in CaMâ??s domain orientation enabled by a flexible linker. Knowing this, the collection and analysis of an extensive set of NOESY spectra is redundant. Although RDCs can define CaM domain orientation in...
nmrlearner Journal club 0 03-03-2011 02:06 AM
[NMR paper] Fast multi-dimensional NMR of proteins.
Fast multi-dimensional NMR of proteins. Related Articles Fast multi-dimensional NMR of proteins. J Biomol NMR. 2003 Apr;25(4):349-54 Authors: Kupce E, Freeman R Three-dimensional HNCO and HNCA subspectra from a small protein (agitoxin, 4 kDa, enriched in carbon-13 and nitrogen-15), have been obtained by direct frequency-domain excitation of selected carbon and nitrogen sites. This new technique applies an array of several simultaneous soft radiofrequency spin-inversion pulses, encoded (on or off) according to nested Hadamard matrices, and the...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR analysis blog] New Fast NMR technique
New Fast NMR technique Instrument time is precious and a plethora of different fast NMR experiments are continuously being proposed in order to reduce the time required to record an NMR spectrum. Actually, money is not the only reason, there are many other factors which motivate the development of techniques to increase the speed of data collection. For example, if one wants to make real-time studies of kinetic processes or protein folding, it’s pivotal to speed up the acquisition of NMR data, in particular multidimensional spectra. On this issue, we have just put our bit into this field...
nmrlearner News from NMR blogs 0 08-21-2010 09:12 PM
[Stan NMR blog] NMR tubes, or how to get poor very fast
NMR tubes, or how to get poor very fast Comments about storing, cleaning and sealing of NMR spectroscopy sample tubes More...
nmrlearner News from NMR blogs 0 08-21-2010 05:42 PM
15N SOFAST-HMQC to study fast H-D exchange
Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds Paul Schanda and Bernhard Brutscher J. Am. Chem. Soc.; 2005; 127(22) pp 8014 - 8015 http://pubs.acs.org/isubscribe/journals/jacsat/127/i22/figures/ja051306en00001.gif Abstract: We demonstrate for different protein samples that 2D 1H-15N correlation NMR spectra can be recorded in a few seconds of acquisition time using a new band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence experiment. This has enabled us to...
nmrlearner Journal club 0 06-21-2005 06:21 AM



Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 01:06 AM.


Map