mddnmr error

[Guillaume LAURENT]

Hello,
I am trying to use mddNMR with qMDD. I have put some data files in my Documents directory, including official examples, in both bruker and agilent format.

When I run qMDD, whatever data file or processing mode I use, I have the following error :

####> mddnmr4pipeN  1 2 3 42
########## conversion from spectrometer format to nmrPipe format ../b_hnco to ./XYZA/ft4sp.xyza.2D
No fid file ../b_hnco
mddnmr4pipeN 1 2 3 42 failed
Error command 'FTx.sh.2D ./XYZA/ft4sp.xyza.2D' failed

Do you have any idea to solve it ?
Thanking you,
Guillaume

[Mark Maciejewski]

Guillaume,

I suspect the issue is with the current working directory not being in your path. Can you answer a question... Are you getting the error while executing the processing scripts from within the qMDD GUI or by executing the scripts built by qMDD from a terminal? 

We have qMDD setup to set the current working directory in your path when it is launched so this problem should not show up when executing processing from within the qMDD GUI. If you are launching the scripts generated by qMDD from a terminal try typing "export PATH=$PATH:." without the quotes first and then execute the script from the same terminal.

Please let me know specifically if you were executing the processing from within the qMDD GUI or from the terminal. If you are getting the error from within the qMDD GUI I will have to dig a bit further. In that case, if you can spell out each of your steps it will be helpful. For example; opened qMDD, pressed "this" button, etc.

Thanks,

Mark

[Guillaume LAURENT]

Dear Mark,

I am just launching qMDD in a terminal, which opens the GUI. I then select a data subdirectory, inside my Documents directory, and just click RUN.

I have the same result when I go to the FID directory before starting the GUI.

However, if I use the menu nmrbox-software/MDD, I have another error:

nmrPipe: Command not found.
Check the software installation and path
mddChecks.sh failed

Cheers,
Guillaume

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[Mark Maciejewski]

Guillaume,

We have identified the problem and will make a fix to the NMRbox VMs soon. In the meantime there is a simple fix to get you going today.

Open a terminal

Enter "export PATH=.:$PATH" without the quotes

From the same terminal type "qMDD"

Open spectrum, navigate to the directory where the ser or fid file exists and open the spectrum

Hit okay if it prompts you about directory already existing

You should see a dialog box about referencing, just hit ok

Click the run button - a FT should begin. It may not look good without changing settings, but the FT should start and not give the error message you reported.

Let me know if this fixes the issue. Note that after we patch the NMRbox VMs the "export PATH=.:$PATH" will no longer be necessary.

Thanks for your patience

Mark

On Thursday, February 1, 2018 at 9:02:12 AM UTC-5, Guillaume LAURENT wrote:

[Weatherby,Gerard]

The MDD launch scripts have been patched to fix the problem Guillaume found.

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Gerard Weatherby
Application Architect
UConn Health
NMRbox | Department of Molecular Biology and Biophysics
263 Farmington Avenue, Farmington, CT 06030-6406
Phone: 860 679 8484

[Guillaume LAURENT]

Thank you for your quick answer and for solving the problem. I just logged out and it is working perfectly.

Cheers
Guillaume

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