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Hello,

I'm currently processing a large amount of T1 and T2 spectra in NMRDraw. I've been looking for a way to copy my peak assignments from one spectrum onto to the others so that I can quickly and accurately match height and volume values, but I've had little luck so far. Is it possible to manipulate the assignment tables to achieve this goal? NMRPipe and its associated applications are all very new to me at this point, so any information that may expand my general knowledge of the program or lead to a solution for the problem outlined above would be appreciated.

Thanks

asked Jul 24 '10 at 17:16

ccantr10's gravatar image

ccantr10
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updated Jul 25 '10 at 10:55


9 Answers:
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I would go for ccpn.

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answered Jul 25 '10 at 22:00

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justin
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You could do this kind of thing using a macro in Felix. Felix has a database where you can store crosspeak information. You would probably start by processing one dataset and creating a crosspeak table that contains all the peak positions. Then you would setup the macro to automatically process and phase correct each matrix, compare peak position information between the reference matrix and the current matrix and optimize center positions if necessary. Then you would store volume or height information for each peak. You could setup the macro to then loop over each matrix in the T1/T2 dataset and calculate the T1/T2 values. Then loop over any number of similar datasets. You could typically automate the entire process.

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answered Jul 25 '10 at 11:46

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Steve
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You can use MestReNova where all the assignments are linked to the molecular structure.

In addition you can copy the peaks (with the assignments) just by Ctrl+C (in the original dataset) and then 'Edit/Paste Properties/NMR Peaks' in the other spectra.

If your question is about T1/T2 analysis, then your feature is 'Data Analysis'

For further information, just email here

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answered Jul 26 '10 at 05:44

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Mestrelab
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updated Jul 26 '10 at 05:47

congrats on the world cup, btw. - Evgeny Fadeev (Jul 26 '10 at 11:42)

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Hi,

Try to use seriesTab utility comes with nmrPipe/nmrDraw. If you need more info check the following link out. We have got a very detailed step-by-step description for the analysis of relaxation data. Basically, You don't have to pick peaks in all the spectra collected using different delays for T1/T2 measurement. All you have to do is peak pick the first spectrum (high intersity). seriesTab will do the rest. It automatically collects intensity info from all the spectra and normalize it. Then you can use any program Excel or Sigmaplot to fit it and extract T1/T2 values. Please let me know if you need more info.

http://nmr.uthscsa.edu/t2n15v1214.shtml

-Ilango.

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answered Jul 27 '10 at 04:27

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Ilango
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There are two ways you can do this using nmrPipe. Both of these methods require that you have a peak table for an assigned HSQC and have peak picked and saved a table for the first spectrum in your series.

  1. You can operate on the raw tables using one of the matchTab.tcl scripts in the nmrPipe com directory. IIRC, the one you want is matchTab2.tcl.

  2. You can use the ipap.tcl script that also lives in the com directory. Use it in the single mode and set the expected y difference to 0 Hz. You can type "ipap.tcl -help" to get the list of flags/inputs you need. This is my preferred method since it will try to make the best match but then let you change or fix anything in a reasonably nice GUI.

You can also fit your intensities for the series using nmrPipe's nlinLS module. The currently suggested way of doing this is with the autoFit.tcl script which will generate the input and do the peak fitting - again type "autoFit.tcl -help" for the options.

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answered Jul 30 '10 at 05:21

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Andrew Fowler
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Sorry to post another response recommending another program, but this should be nigh trivial in NMRViewJ.

You'd just open up your first spectrum in the series, open up your peak list with "Peaks...File..Read List". If the spectrum you're examining is NOT the one you picked the peaks on, all you do is go to "Peaks...Integrate...Associate Dataset", and choose the new spectrum this peaklist should be associated with. "Peaks...Integrate...Get Volumes" then integrates the peaks! Voila! I've done this a lot when assigning spectra of proteins with highly similar spectra.

The NMRVIewJ "Analysis...Rate Analysis" tool can then be used to get your T1 and T2 data easily.

Give it a try! Converting NMRPipe data to NMRView format is easy. I think the script/command is commonly called "pipe2view.com" Here are its non-cmment line contents: nmrPipe -in ./test.ft \ |pipe2xyz -out test.nv -nv

Hope this helps!

  • Josh
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answered Aug 06 '10 at 03:58

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http://spin.niddk.nih.gov/NMRPipe/doc2new/#How to fit pseudo 3D spectra http://www.youtube.com/user/NMRFAM

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answered Sep 07 '10 at 18:33

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GC
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I had this problem befor. We used ipap.tcl, this way you can prpagat the assignment between peaklists. You can see if the assignment is correct graphically and confirm if it´s OK.

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answered Sep 09 '10 at 10:09

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Marcos
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Hello,

Unfortunately I can't answer for nmrDraw, because I only use it when I process data (FT, etc) with nmrPipe.

Maybe you'll benefit by changing your title to something like "Software to analyze 2D T1 and T2 relaxation rate data?" - that way the question will probably attract answers about other programs.

At the 50th ENC Clemens Anklin showed a program written at Bruker that does that sort of analysis easily. Links (must register on Bruker site to access): windows version and linux version.

If I had to do this analysis myself I would use Sparky. Mostly because of familiarity and the mechanical memory of typing commands. Hand-typed commands in sparky give you very fast access to all functions of the software.

Copy-pasting peaks in sparky from one spectrum to another is very simple (click into first spectrum, type pa - select all peaks, oc - copy peaks - ornament copy, click into another spectru and type op - paste). Command pi integrates selected peaks - runs fitting and calculates peak volumes. Command it - gives access to options used by the integration algorithm.

You can select multiple peaks by holding Shift key while clicking on the peaks.

The fitting routine moves peak positions to fit the data better - and it is not always accurate at that. If you don't want the peaks to move then you can lock the by typing pk. Command pu unlocks peaks.

You can integrate peaks either one-by-one or in bulk - depending on how many are selected. When peaks overlap then they need to be fitted simultaneously.

If you want peak volumes then it's a very good idea to check the quality of peak fitting. IMO even the best fitting algorithms will fail when fitting areas with many overlapped peaks.

In sparky you can turn on display of X and Y 1D slices by typing vS - when you put your mouse over the peak you will see 1D lines of real data and fitting curves.

In the end you will have several spectra with picked and integrated peaks. Command lt opens the peak list which can be saved in the text format and you can select what goes into the spectrum.

Sparky does not provide means to analyze multiple peak tables - you'll have to do that externally with whatever tool you prefer - e.g. excel, your own perl/python/tcl scripts, etc.

Well - as you can see - sparky gives access to many "low-level" functions via short hand-typed commands (they are also accessible through menus though). Probably learning enough of those commands is the biggest part of the learning curve, but IMO it is still easier than learning how to navigate through complex user interfaces - by clicking on menus, buttons, etc.

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answered Jul 25 '10 at 09:51

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
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updated Aug 06 '10 at 09:59

Hi here is the link to the program: http://www.bruker-biospin.com/sw_nmr_win_protein.html http://www.bruker-biospin.com/sw_nmr_linux_protein.html you need to register on the site to get access. - Clemens Anklin (Jul 28 '10 at 02:12)

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