mddnmr in macOS X El Capitan

[Samantha Lagaida]

Hi All, 

I installed the newest version of qMDD in macOS X El Capitan recently. The program works as I can call the GUI in terminal. However, I only got one spectrum (filename.ft) after I run the program. I tried to run in Zero mode, MDD mode and CS mode with default setting and I still only get one spectrum.

Based on the manual, I know that I should get three more spectrum to do the phasing. 

I wonder if there is any way to fix this since I can't do the proper phasing in .ft file. 

Any help would be appreciated :)

Regards, 

Sam 

[Vladislav Orekhov]

Hi Sam,
GUI produces script for processing.
2D projections from 3D and 4D spectra, which you may use for phasing, are produced by line  

proj3D.tcl -in ft/test%03d.dat

in the main script proc.sh .
proj3D.tcl  is a routine from nmrPipe package. A typical reason for proj3D.tcl to fail is wrong labeling of the spectra axis. The labeling is defined in the nmrPipe script  fidSP.com. It looks like :

-xLAB           H1              -yLAB           C13             -zLAB           N15              \

proj3D.tcl uses the labels to make file names, thus  please do not use symbols that cannot be used in file name, e.g. C=O.

Regards,
Vladislav

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[Samantha Lagaida]

Hi Vladislav, 

Thanks for your reply.I changed the label in fidSP.com and I attached a copy of it. 

But I'm still missing those three files. 

I am missing these lines in the log:

Reading Projection: H/C=O

Reading Projection: H/N

Reading Projection: C=O/N

Writing Projection: H.C=O.dat

Writing Projection: H.N.dat

Writing Projection: C=O.N.dat

I guess that's why I didn't get those files

Cheers,, 

Sam 

[Vladislav Orekhov]

Hi Samantha,
error

 proj3D.tcl -in ft/test%03d.dat

dyld: Library not loaded: /usr/local/nmr/lib/libtk8.4.dylib

  Referenced from: /Applications/nmrpipe/nmrbin.mac/nmrWish

  Reason: image not found

shows that you indeed are missing the library or the LD path is wrong. This is related to your installation of nmrPipe package. I suggest that you download and install the latest version of nmrPipe.

Regards,
Vladislav

On 2016-07-13 15:02, Samantha Lagaida wrote:

Hi Vladislav, 

Sorry for the confusion. I tried to process the data in other computer (Linux), just to check whether my actual data is OK. So when I run the data in linux, the program produces 4 files. So, I compared between the linux's log and my mac log and found the missing lines. 

I didn't change the label in Linux, that's why the label still C=O, etc

Anyway, I run the nmrPipe command and I got these :

[Samanthas-MacBook-Pro:NMR Q1/20160707_Q1/2.proc] Kuroyama% showhdr ft/test001.dat

FILE: ft/test001.dat DIM: 3 QUAD: Real 2DMODE: States Not Transposed

BYTES: 207872 PRED: 207872 MIN: 0 MAX: 0 VALID: 0

ORDER: 2 1 3 PIPE: 0 CUBE: 0 FILES: 64 804x64x1 2D Series

               X-Axis        Y-Axis        Z-Axis   

DATA SIZE:           804           64           64

APOD SIZE:           402           24           32

SW Hz:       3774.789795  1609.787964  2107.926025

OBS MHz:      800.130005   201.192993    81.075996

ORIG Hz:     4800.609375 33926.050781  8668.690430

DOMAIN:             Freq         Freq         Freq

MODE:               Real         Real         Real

NAME:                 H1          C13          N15

[Samanthas-MacBook-Pro:NMR Q1/20160707_Q1/2.proc] Kuroyama% showhdr 2.ft3

FILE: 2.ft3 DIM: 3 QUAD: Real 2DMODE: States Not Transposed

BYTES: 13174784 PRED: 13174784 MIN: 0 MAX: 0 VALID: 0

ORDER: 2 1 3 PIPE: 1 CUBE: 0 FILES: 1 804x64x64x1 3D Stream

               X-Axis        Y-Axis        Z-Axis   

DATA SIZE:           804           64           64

APOD SIZE:           402           24           32

SW Hz:       3774.789795  1609.787964  2107.926025

OBS MHz:      800.130005   201.192993    81.075996

ORIG Hz:     4800.609375 33926.050781  8668.690430

DOMAIN:             Freq         Freq         Freq

MODE:               Real         Real         Real

NAME:                 H1          C13          N15

I think the label changed successfully. But when I run proj3D.tcl -in ft/test%03d.dat. I got error:

[Samanthas-MacBook-Pro:NMR Q1/20160707_Q1/2.proc] Kuroyama% proj3D.tcl -in ft/test%03d.dat

dyld: Library not loaded: /usr/local/nmr/lib/libtk8.4.dylib

  Referenced from: /Applications/nmrpipe/nmrbin.mac/nmrWish

  Reason: image not found

Trace/BPT trap

Do you know how to get these libraries?

Cheers, 

Sam

On Wed, Jul 13, 2016 at 10:49 PM, Vladislav Orekhov <vl.or...@gmail.com> wrote:

Hi,
I am a bit confused. The file qMDD.txt that you sent me looks as OK fidSP.com . On the other hand, lines like 

Reading Projection: H/C=O
Writing Projection: H.C=O.dat

Indicate that you have a label "C=O" , which is not allowed.
Could you run command

proj3D.tcl -in ft/test%03d.dat

in terminal window in the directory *.proc ?
I assume you have files ft/test???.dat and  fidname.ft3. You can see actual labels by running nmrPipe command

showhdr ft/test001.dat
showhdr fidname.ft3

/Vladislav