BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > NMR Questions and Answers
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 Rating: Thread Rating: 1 votes, 5.00 average. Display Modes
  #1  
Unread 10-07-2010, 12:49 AM
Junior Member
 
Join Date: Oct 2010
Posts: 1
Points: 12, Level: 1
Points: 12, Level: 1 Points: 12, Level: 1 Points: 12, Level: 1
Level up: 23%, 38 Points needed
Level up: 23% Level up: 23% Level up: 23%
Activity: 20.0%
Activity: 20.0% Activity: 20.0% Activity: 20.0%
NMR Credits: 64
NMR Points: 12
Downloads: 0
Uploads: 0
Default Unanswered: 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 differently to the data, that I should correct for in Matlab?

Thanks
Reply With Quote


Did you find this post helpful? Yes | No

  #2  
Unread 10-17-2010, 10:09 PM
markber's Avatar
Administrator
 
Join Date: Oct 2008
Posts: 1,538
Points: 35,627, Level: 100
Points: 35,627, Level: 100 Points: 35,627, Level: 100 Points: 35,627, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
Last Achievements
NMR Credits: 1,550
NMR Points: 35,627
Downloads: 17
Uploads: 4
Default

A relevant discussion at NMRWiki can be found at

Processing 1D FID of ethanol exported from spinworks - NMR Wiki Q&A Forum
Reply With Quote


Did you find this post helpful? Yes | No
Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Exploring the trigger sequence of the GCN4 coiled-coil: biased molecular dynamics resolves apparent inconsistencies in NMR measurements.
Exploring the trigger sequence of the GCN4 coiled-coil: biased molecular dynamics resolves apparent inconsistencies in NMR measurements. Exploring the trigger sequence of the GCN4 coiled-coil: biased molecular dynamics resolves apparent inconsistencies in NMR measurements. Protein Sci. 2010 Dec;19(12):2462-74 Authors: Missimer JH, Dolenc J, Steinmetz MO, van Gunsteren WF Trigger sequences are indispensable elements for coiled-coil formation. The monomeric helical trigger sequence of the yeast transcriptional activator GCN4 has been investigated...
nmrlearner Journal club 0 03-13-2011 04:01 AM
[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
[NMRwiki tweet] nmrwiki: How to analyze T1 recovery with MatNMR? http://qa.nmrwiki.org/question/201/
nmrwiki: How to analyze T1 recovery with MatNMR? http://qa.nmrwiki.org/question/201/ nmrwiki: How to analyze T1 recovery with MatNMR? http://qa.nmrwiki.org/question/201/ Source: NMRWiki tweets
nmrlearner Twitter NMR 0 11-18-2010 06:16 PM
[Question from NMRWiki Q&A forum] T1 Recovery Law with matNMR
T1 Recovery Law with matNMR Hi everybody,I can't figure out how to do this in matNMR: I've 32 echoes with different tao separating the pi/2 impulses. This 32 measurements shows an increasing peak which reach saturation. I'd like to extract the value of T1 from my recovery law but I can't understand how to use the T1 fit option with this measurements. ThanksPietro
nmrlearner News from other NMR forums 0 11-18-2010 06:16 PM
[Question from NMRWiki Q&A forum] MatNMR for a 2D Spectrum
MatNMR for a 2D Spectrum Hi, Does anyone have experience using MatNMR to produce a 2D spectrum? Or know of any examples? I'm trying to follow the instructions in the documentation: http://matnmr.sourceforge.net/manual/Processing.html#Intro for the sample data, but there are a few things I can't get to work. I use FT from the 2D menu which seems to take the Fourier transform along the TD2 direction. In the documentation is says to then take the Fourier transform along the TD1 direction, but when I use FT it seems to take it along the TD2 direction again.
nmrlearner News from other NMR forums 0 10-28-2010 09:02 AM
[Question from NMRWiki Q&A forum] 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...
nmrlearner News from other NMR forums 0 10-05-2010 02:11 PM
MatNMR exporting data problem
Hi all, I'm trying to extract the data (Bruker TopSpin) into excel or origin. I don't have access to the NMR machine right now to use its interface software. So I am using MatNMR. I am able to load the FID (1D) then do FT and PHASE. How can I have the data of the final spectrum screen, so that I can draw it by excel or origin. Is there any way to do this?:confused: Thanks in advance.
amin5236 NMR software 0 04-01-2010 01:33 PM
No spontaneous blindness with matNMR anymore
matNMR, a good program for analysis of 1D and 2D spectra, has now a new color scheme (to address "the spontaneous blindness" issue) as well as many bug fixes and functionality improvements. The latest version of matNMR was released on May 5th, 2005. Read introductory information about matNMR from its website below. MatNMR is more than a static program that can be used only for processing data. It offers a wide variety of commonly used processing techniques for 1D and 2D spectra and combines these with the powerful graphical and numerical possibilities of MATLAB. Basically the concept...
nmrlearner NMR software 0 05-20-2005 05:52 AM


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 - 2017, 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 06:06 PM.


Map