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 01-18-2011, 02:44 AM
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 First-Order Phase Errors

First-Order Phase Errors

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.



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
[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 Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 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 More...
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.
nmrlearner NMR dynamics 0 05-07-2005 09:21 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 12:44 AM.


Map