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 other NMR forums
Advanced Search



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 10-05-2010, 02:11 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,903
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 Processing 1D FID of ethanol exported from spinworks

Processing 1D FID of ethanol exported from spinworks

Hello,

This is probably a basic question, alas it has caused considerable turmoil, so at the risk of embarrassing myself. . . I am trying to implement some algorithms for processing NMR spectra using Matlab.

I got data for the 1D FID of ethanol from the biomolecular magnetic resonance database which, as far as I can tell, is in the Bruker format. I opened the file in spinworks without problems and used the "export xy data" function to get a text file of what appears to be the real channel(?)

I loaded this into Matlab and the intially the FID appeared to be the same, but there are some differences from that which is produced by spinworks.

(1) There are negative time values.

(2) I took the Fourier transform (using the fft() fuction in Matlab), and from the exported data file found a field that appears to be the reference frequence (400MHz ish?), so I adjusted the frequencies to be (frequency - reference)/reference. The frequency values have a factor of 1e4 attached though, and even worse are a bit different from those in spinworks, (3ppm instead of 5ppm etc.). The overall shape and difference between the peaks is just like the spinworks spectrum though.

(3) Also there only appears to be a real channel. . . Am I supposed to take a Hilbert transform? Or is the imaginary channel hiding somewhere?

My feeling was that maybe spinworks exports the "raw" uncorrected data from the Bruker file and they are full of Bruker eccentricities that I should correct for in order to get the right data. If this is the case, is there somewhere I can find out the things I need to correct for? And additionally, is simply using the FFT directly, oversimplifying what's required to get a spectrum, or am I on the right track?

Sorry for the incredible long winded post by the way. . .

Thanks in advance



Check if somebody has answered this question on NMRWiki QA forum
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: processing hmbc
Re: processing hmbc Thank you, Andrew, very much!! I will try this. I am using hmbcetgpnd from Bruker, which is almost the same as I guess. Thank you for very helpful comments More...
NMRpipe Yahoo group news News from other NMR forums 0 10-20-2011 09:51 PM
[NMRpipe Yahoo group] Re: processing hmbc
Re: processing hmbc Thanks for this thorough and helpful response from Andrew. Just to amplify one item ... the nmrPipe "FT" function will work with any number of points. It will More...
NMRpipe Yahoo group news News from other NMR forums 0 10-20-2011 09:51 PM
[NMRpipe Yahoo group] Re: processing hmbc
Re: processing hmbc Anna Kuznetsova asks about processing an HMBC. I think the key quote is "So instead of many absorptive peaks of HMBC I get 4 times more peaks with alternating More...
NMRpipe Yahoo group news News from other NMR forums 0 10-20-2011 09:51 PM
[NMRwiki tweet] nmrwiki: Spinworks updated - improved baseline correctionhttp://nmrwiki.org/wiki/index.php?title=SpinWorks
nmrwiki: Spinworks updated - improved baseline correctionhttp://nmrwiki.org/wiki/index.php?title=SpinWorks nmrwiki: Spinworks updated - improved baseline correctionhttp://nmrwiki.org/wiki/index.php?title=SpinWorks Source: NMRWiki tweets
nmrlearner Twitter NMR 0 02-10-2011 08:25 AM
[NMRpipe Yahoo group] Re: Help in processing
Re: Help in processing You can find a list of NMRPipe functions and commands here: http://spin.niddk.nih.gov/bax/software/NMRPipe/ref/ In particular, the programs of NMRPipe are More...
NMRpipe Yahoo group news News from other NMR forums 0 01-13-2011 01:52 AM
[NMRpipe Yahoo group] Help in processing
Help in processing Hi, I have two 2D NMR data which I want to process in a fancy way. 1) First FT along t2 dimension for both two 2D data acquired in magnitude mode. 2) Divide More...
NMRpipe Yahoo group news News from other NMR forums 0 01-13-2011 01:52 AM
Spinworks and MatNMR Inconsistencies
Hello, I'm pretty new to NMR, and am just trying to do some simple data processing with a 1D ethanol spectrum I got from a Bruker spectrometer. I opened it in Spinworks and it appears to be normal, when I take the Fourier transform the spectrum is what I expected. I wanted to process this in Matlab however, so I used MatNMR to load the FID into Matlab. It seems though, that a lot of the data is for negative time values. When I take the Fourier transform it looks quite different and is considerably more noisy. Given that the data is the same, is there something that spinworks does...
jeffery NMR Questions and Answers 1 10-17-2010 10:09 PM
[NMR paper] Direct binding of ethanol to bovine serum albumin: a fluorescent and 13C NMR multiple
Direct binding of ethanol to bovine serum albumin: a fluorescent and 13C NMR multiplet relaxation study. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Direct binding of ethanol to bovine serum albumin: a fluorescent and 13C NMR multiplet relaxation study. Biochemistry. 1996 Jan 9;35(1):340-7 Authors: Avdulov NA, Chochina SV, Daragan VA, Schroeder F, Mayo KH, Wood WG Molecular mechanisms of ethanol interaction with proteins are not well-understood. In the present study, direct...
nmrlearner Journal club 0 08-22-2010 02:27 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

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 On
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 - 2020, 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 03:10 PM.


Map