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  
Unread 12-05-2015, 01:26 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,174
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 Stanning: A new NMR apodization function

Stanning: A new NMR apodization function




Apodization refers to the mathematical processing technique by which the FID is multiplied pointwise by some appropriate function in order to improve the instrumental line shape. The term apodize actually derives from its Greek meaning “removing the feet”. The feet being referred to are actually the side-lobes found in the FT spectrum resulting from zero-filling a truncated FID (this phenomenon is also known as leakage).
Probably the most widely used apodization function in NMR, especially in 13C spectroscopy, is the Exponential function although other functions such as Hanning are also very popular.
In this short post, I want to introduce a new apodization function, the so-called Stanningfunction which gives superior results compared to Exponential and Hanning apodization functions.
The name Stanning is a play on words which combines Hanning (which forms the basis of this function) with Stan, the inventor of this apodization function to whom all credit should be given.
The performance of this apodization function is illustrated with a 19F NMR spectrum whose FID is shown in Figure 1.


Figure 1

This FID consisted of ca 59K acquired data points which are then extended by zero filling to a final size of 128K. As the FID has not fully decayed to zero during acquisition, resulting FT spectrum will show the expected truncation artefacts, as shown in Figure 2.


Figure 2Multiplication of the FID by an exponential function, in this case with a line broadening value of 1.0 Hz results in the following spectrum where the wiggles have been significantly reduced but not in a totally satisfactory way (see Figure 3).


Figure 3

Application of the new Stanning function yields the result depicted in Figure 4. As it can be seen, the truncation artifacts have been further reduced whilst the resolution of the spectrum is slightly better compared to the exponential function.


Figure 4

The mathematical formulation of Stanning as well as some additional illustrative examples will be covered in a future blog post.


More...

Source: NMR-analysis blog
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMRpipe Yahoo group] Re: MED function error.
Re: MED function error. Hi Jason, Thanks very much for bringing this problem to my attention ... sorry, I (yes, even I) made what we call in the trade a "+ 1" "- 1" kind of mistake More...
NMRpipe Yahoo group news News from other NMR forums 0 07-05-2012 04:13 AM
[NMRpipe Yahoo group] MED function error.
MED function error. Dear Frank, We are experiencing segmentation faults in recent versions of NMRPipe on Mac OS X (10.6.8) when using the MED function. An example 2D processing More...
NMRpipe Yahoo group news News from other NMR forums 0 07-04-2012 01:08 AM
[Stan NMR blog] FID apodization and ratios of peak integrals
FID apodization and ratios of peak integrals Review of a sometimes controversial point in NMR spectroscopy practice Source: Stan blog library
nmrlearner News from NMR blogs 0 11-24-2010 07:12 AM
[Stan NMR blog] FID apodization and peak integral ratios
FID apodization and peak integral ratios Review of a sometimes controversial point in NMR spectroscopy practice Source: Stan blog library
nmrlearner News from NMR blogs 0 11-23-2010 07:11 PM
[NMR paper] Using NMR as a probe of protein structure and function.
Using NMR as a probe of protein structure and function. Related Articles Using NMR as a probe of protein structure and function. Biochem Soc Trans. 1999 Aug;27(4):701-13 Authors: Malthouse JP
nmrlearner Journal club 0 11-18-2010 08:31 PM
[Stan NMR blog] Three-point interpolation of a real function
Three-point interpolation of a real function C code including coordinate estimates and reliability of local minima/maxima. More...
nmrlearner News from NMR blogs 0 08-21-2010 06:14 PM
[Stan NMR blog] New asymptotic expansion for the Gamma function
New asymptotic expansion for the Gamma function G.Nemes, a young Hungarian mathematician, presents a novel Gamma-function series and a closed-form approximation formula. More...
nmrlearner News from NMR blogs 0 08-21-2010 06:14 PM
Finding protein function from its NMR structure
For proteomics folks who gamble with their careers by promising discovery of protein function from NMR structures that may not look like any known proteins. Find the best structural matches in a protein database DALI CE DEJAVU Align structure of your protein with several proteins of your interest MASS MaltiProt
nmrlearner Structural analysis 1 09-19-2006 12:11 PM



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 08:27 AM.


Map