Re: REV_option_MDD

[Tomas Sikorsky]

try

| nmrPipe -fn FT -alt

or

| nmrPipe -fn FT -alt -neg

Dne pátek, 21. prosince 2012 19:04:28 UTC+1 dongre napsal(a):

Hi everybody,
 Recently i have acquired 15n 3-D noesy in bruker spectrometer (topspin 3.0).
 I could process the spectra with qMDD(2.2 version I guess, recent update) but i observed that proton axis in indirect dimension is reversed. Does any body knows how to fix this problem in MDD.
I tried using,

| nmrPipe -fn FT -neg \ and nmrPipe -fn REV -sw, independently but no success.
looking forward for the reply.
I also checked one of the treads in the this group looking for the same thing but i could not find the solution.
best regards,
Ramachandra 

[Vladislav Orekhov]

Hi,
one of
  | nmrPipe -fn FT -alt  \ nmrPipe -fn FT -neg \ and nmrPipe -fn REV -sw
should work.
The problem, however, may be if in your unix path has ${MDD_NMR}/com before the current directory, in which case ${MDD_NMR}/com/recFT.com
is used instead of ./recFT.com and your changes do not work.

Vladislav

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[ramachandra dongre]

Dear Tomas and Vladislav, Thank you for your reply.

But the corrections suggested do not work, i think what Vladislav suspecting is right.

so my next question is how to fix this, how that path should look like...?

is it should be "${MDD_NMR}/recFT.com" ?

best regards

Rama

--
Ramachandra Dongre
PhD student (AIO)
NMR Spectroscopy Research Group
Bijvoet Center for Biomolecular Research
Utrecht University
Bloembergen gebouw
Padualaan 8, 3584 CH Utrecht
Telephone: +31.(0)30.2532875
 Fax: +31.(0)30.2537623
E-mail: -------@nmr.chem.uu.nl
The Netherlands

[ramachandra dongre]

my present path is " set path=( $path $MDD_NMRbin  ${MDD_NMR}/com/ ) "

[rharris]

Hi Rama
This was in the older versions of MDDNMR to put in your .cshrc:
set path=( $path . ${MDD_NMR}/bin ${MDD_NMR}/com )

I think that is what Vladislav is suggesting making sure the current directory is read first

richard

[Vladislav Orekhov]

Hi Rama,
you need to make sure that mddnmr4pipeN.sh, which is called in proc.sh, uses recFT.com from the directory where you process the spectrum (working directory). I assume that you edit recFT.com in the working directory. First,  check which recFT.com is actually used 
For this in the working directory give  command
   which recFT.com
If needed, correct the path appropriately and check again. You may need also to run
   source ~/.cshrc
or even logout and login.

Regards,
Vladislav

[Maxim Mayzel]

Hi Rama, 

The general rule, when you add something to the path should be 

set path = ( $path $NEW_DIRECTORY ) ,
but be sure that you have '.'  (almost) at the very beginning of your path. If you don't have '.' in your $path, add
set path = ( '.' $path ) 
at the very beginning of your .cshrc

Regards,
Maxim