The phase of a signal in an NMR spectrum is described here and is determined by the axis on which the magnetization vector resides after the observe pulse relative to the receiver. The phase of the spectrum is typically corrected such that the peak in the real spectrum is entirely in absorption mode while that in the imaginary spectrum is entirely in dispersion mode. The correction in phase is referred to as the zero-order phase correction. A zero-order phase correction applies to all peaks in the spectrum regardless of their offset, ?, from resonance. There are also first-order phase errors where the phase error for a resonance is linearly dependant on ? and the duration of the pulse, tp. The further a peak is away from the center of the spectrum for a given pulse duration, the larger the first-order phase error. Similarly, the longer the duration of the pulse for a peak of given offset, the larger the first-order phase error. These errors arise from the fact that a 90° pulse of fixed duration is only a true 90° pulse for a peak on-resonance. For off-resonance peaks, the pulse will not only be slightly less than 90° but also produce a small amount of magnetization along the axis of the pulse. For example, a 90°x pulse applied to an equilibrium magnetization vector will produce only –y magnetization for an on-resonance signal but for an off-resonance signal, it will also leave a small amount of residual z magnetization as well as produce some x magnetization. It is the x magnetization that gives rise to the first order phase error. The effect of the pulse duration for a peak of given offset frequency is demonstrated in the figure below. The sample was a mixture of chloroform and acetone. The transmitter was set such that the chloroform signal was on-resonance. Six 90° pulses were calibrated at different power levels based on the on-resonance chloroform signal, ranging from 10 µsec in the lower trace to 320 µsec in the upper trace. For all spectra, the same zero-order phase correction was applied such that the chloroform signal was in-phase. No first-order phase correction was applied. One can see that the phase error in the off-resonance acetone signal increases as a function of the pulse duration. It should also be noted that the overall intensity of the acetone signal decreases with respect to the chloroform signal as a function of the pulse duration due to the width of the excitation profile decreasing as a function of the pulse duration.
[Question from NMRWiki Q&A forum] same parameters but difference in phase why?
same parameters but difference in phase why?
hi, though this question seems to be easy for you but i am new for this software and to this field. Recently, i took silicon spectra in 500mhz(bruker) seems to be good (i.e.one silicon peak and one nmr tubes broad peak) but when i used same parameters for another sample where i got single peak as i expected but nmr tube peak is inverse this time. I just copied previous parameters only why i got such a inverse signal.If anybody know please help me.
thank you
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nmrlearner
News from other NMR forums
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03-31-2011 09:21 PM
[NMRpipe Yahoo group] phase problem with trosy-hncacb
phase problem with trosy-hncacb
Dear All: I have this strange phase problem with trosy-hncacb collected on a bruker machine. the HC and HN projection looks good. However, Using the phase
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NMRpipe Yahoo group news
News from other NMR forums
0
03-15-2011 05:56 AM
[U. of Ottawa NMR Facility Blog] The Phase of an NMR Spectrum
The Phase of an NMR Spectrum
Most students know that the phase of an NMR spectrum has to do with the degree to which the NMR resonances are above or below the baseline of the spectrum (i.e. the amount of absorption and dispersion character). Most students have also learned that the phase of a periodic time domain function depends only on the value of the function at time zero. Thus, the only difference between a cosine and a sine function is where the function starts at time zero. A sine is said to be 90° out of phase with respect to a cosine. Many students do not understand the connection...
nmrlearner
News from NMR blogs
0
11-19-2010 06:22 AM
The war of tools: how can NMR spectroscopists detect errors in their structures?
The war of tools: how can NMR spectroscopists detect errors in their structures?
Edoardo Saccenti and Antonio Rosato
Journal of Biomolecular NMR; 2008; 40(4) pp 251 - 261
Abstract:
Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we examined various tools for the assessment of structural quality to ascertain the extent to...
linawaed
Journal club
0
08-04-2008 04:09 AM
Order tensor
Hello,
I have some questions regarding the alignment matrix and I will be very much grateful if you could clarify my doubts.
Question 1:
1) I like to calculate the angle between the magnetic field and X,Y & Z axes of the alignment frame. For that, I have run PALES and got the values for Sxx, Sxy, Sxz, Syy & Syz. From Sxx value I have calculated cos(tx) and cos(ty) from Syy. Substituting these values in 1/2(3cos(tx)*cos(ty)), I calculated Sxy. But, this calculated value does not match with Sxy obtained from PALES.
Question 2:
I found that the saupe parameters are in the order of 10...
tmc
NMR Questions and Answers
1
08-11-2006 07:28 PM
Refinement against order parameter with XPLOR
New 2.10 release of XPLOR-NIH can now do a refinement against order parameters. You can get an idea what this refinement can be used for from the this paper.
Info about new features of XPLOR-NIH 2.10 from XPLOR-NIH website: - new parameter/topology file naming convention: NMR protein refinement should now use topology file protein.top and parameter file protein.par.
- new command: tclXplor which calls xplor -tcl. Can be used as command interpreter
- new potential term OrderPot to enable refinement against order parameters.
- update to PrePot from Junji Iwahara
- CSAPot: 15N CSAs...
nmrlearner
NMR structure calculation
0
05-16-2005 04:02 AM
Script to obtain order parameters from a structure
A Python script for prediction of order paramter from a structure is available from this website.
The script is based on the following paper
F. Zhang and R. Brüschweiler (2002) "Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins" J. Am. Chem. Soc. 124(43), 12654-12655.