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 01-21-2011, 03:31 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,700
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 Excitation Profiles for Shaped Pulses

Excitation Profiles for Shaped Pulses

Shaped pulses are very commonly used for selective excitation and nonselective inversion in a large number of NMR pulse sequences. The frequency domain excitation profile of a radio frequency pulse is the Fourier transform of the time dependent pulse shape and determines the width, uniformity and phase of the frequency spectrum excited. Since time and frequency are reciprocals of one another, short rf pulses have very wide excitation profiles and long rf pulses have very narrow selective excitation profiles. In a previous BLOG post the excitation profiles of rectangular pulses of varying duration were determined experimentally. The Fourier transform of a rectangular pulse is a sinc function which is observed to be the experimentally determined excitation profile. Short high power rectangular pulses are very desirable for uniform excitation over wide frequency ranges as the entire NMR spectrum of interest usually occupies only a very small central portion of the central lobe of the sinc shaped excitation profile which, to a first approximation, is flat over the observed spectral width. Rectangular pulses are often not desirable when narrow excitation profiles are required as the excitation is not uniform over the desired region and the ripples of the sinc excitation profile cause nodes of excitation and negative peaks.

The Fourier transform of a sinc function is a box function, so if a long low power sinc shaped rf pulse is used one obtains a narrow flat box shaped excitation profile. This is indeed the case as can be seen in the bottom trace of the figure below. The trace is composed of a series of 1H NMR spectra of H2O/D2O where a truncated, 200 msec, 10 cycle sinc shaped monochromatic rf pulse was applied with varying rf frequency offsets. One can see that the excitation profile is, to a good approximation, a narrow flat box function. The deviation from a flat box function is the result of the truncation of the sinc pulse. It should be noted that the phase of the resonances is not constant across the excitation profile. Sinc pulses are not frequently used for selective excitation because of the phase problem and the fact that very long, minimally truncated pulses must be used. A frequently used alternative to the sinc pulse for selective excitation is the Gaussian shaped pulse. The Fourier transform of a Gaussian is a Gaussian and one therefore will obtain a narrow Gaussian shaped excitation profile when a long low power Gaussian shaped pulse is used. This is shown in the top trace of the figure below. This trace is similar to the bottom trace except a 20 msec Gaussian shaped pulse (with truncation at 1 % of the total height) was used rather than a 200 msec sinc pulse. Although the excitation is not flat, the phase is constant across the excitation profile and the total duration of the pulse is 10 times shorter than the sinc pulse.



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
NMR Excitation, Dephasing and Spin Echoes
NMR Excitation, Dephasing and Spin Echoes http://i.ytimg.com/vi/KtWnmFg-u5g/default.jpg NMR Excitation, Dephasing and Spin Echoes This short animation shows the process of NMR excitation in the laboratory and the rotating frame, as well as the dephasing that occurs from field inhomogeneity and the formation of the Hahn spin echo. Please credit (c)2010 Mark Cohen (mscohen@ucla.edu) during re-use. From:markcat3t Views:8653 http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif...
nmrlearner NMR educational videos 0 01-29-2012 07:45 PM
[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
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins.
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins. Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins. Prion. 2011 Jul 1;5(3) Authors: Santo KP, Berjanskii M, Wishart DS, Stepanova M Abstract Collective motions on ns-?s time scales are known to have a major impact on protein folding, stability, binding and enzymatic efficiency. It is also believed that these motions may have an...
nmrlearner Journal club 0 08-27-2011 04:53 PM
[U. of Ottawa NMR Facility Blog] Shaped Pulses
Shaped Pulses Shaped rf pulses are used frequently in modern NMR experiments for selective excitation and more efficient inversion. The figure below shows some of the pulse shapes in the Bruker shape library measured with an oscilloscope on an AVANCE III console. Each 50.3 MHz rf pulse was 1 msec in duration and was measured at the output of the signal generation unit.http://2.bp.blogspot.com/--GjbnC0soco/TeU9TDXS7nI/AAAAAAAAA4c/Kt3DwPKLjx8/s400/shaped_pulses_scope.jpghttps://blogger.googleusercontent.com/tracker/3300702123878659843-4230712340261495616?l=u-of-o-nmr-facility.blogspot.com...
nmrlearner News from NMR blogs 0 05-31-2011 11:41 PM
[U. of Ottawa NMR Facility Blog] FT NMR Spectra Without Pulses
FT NMR Spectra Without Pulses An FT NMR spectrum is obtained by applying a pulse at the Larmor frequency to a sample in a magnetic field. The precession of the spins induces a voltage in the receiver coil which is recorded as a function of time. The Fourier transform of the time dependent signal is the NMR spectrum. What happens if you do not provide any pulses? You might think that you would not observe a signal - but this is not the case. Even without any pulses there is sufficient noise present to allow incoherent precession of the nuclear spins. This precession can be measured and...
nmrlearner News from NMR blogs 0 04-19-2011 02:44 AM
[Question from NMRWiki Q&A forum] Software to create shaped pulse files from mathematical equation?
Software to create shaped pulse files from mathematical equation? I would like to create working shaped pulse files in one step starting from mathematical expressions - one for amplitude, another for phase vs. time. Does anyone know software that can do it? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 04-12-2011 01:10 PM
Metabolic profiles show specific mitochondrial toxicities in vitro in myotube cells
Metabolic profiles show specific mitochondrial toxicities in vitro in myotube cells Abstract Mitochondrial toxicity has been a serious concern, not only in preclinical drug development but also in clinical trials. In mitochondria, there are several distinct metabolic processes including fatty acid β-oxidation, the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS), and each process contains discrete but often intimately linked steps. Interruption in any one of those steps can cause mitochondrial dysfunction. Detection of inhibition to OXPHOS can be complicated in...
nmrlearner Journal club 0 03-03-2011 02:06 AM
[NMR paper] Improved excitation pulse bandwidths using shaped pulses, with application to heteron
Improved excitation pulse bandwidths using shaped pulses, with application to heteronuclear half filters in macromolecular NMR. Related Articles Improved excitation pulse bandwidths using shaped pulses, with application to heteronuclear half filters in macromolecular NMR. J Magn Reson B. 1995 Jul;108(1):12-21 Authors: Hyre DE, Spicer LD The advantageous use of sinc-shaped pulses in heteronuclear half filters is explored for studying biological macromolecules. The typical square, or hard, pulse used in half-filter pulse sequences for...
nmrlearner Journal club 0 08-22-2010 03:41 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 12:28 PM.


Map