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Re: [nmrpipe] Bruker Style Pseudo3D data processing macro

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  • ASOKAN ANBANANDAM
    Hi Frank, Thank you very much. Your suggestion helped me to solve the problem. In fact, the pulse sequence header file has acquisition order as 312, which I
    Message 1 of 3 , Sep 1, 2009
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      Hi Frank,
      Thank you very much. Your suggestion helped me to solve the problem. In fact, the pulse sequence header file has acquisition order as 312, which I did NOT see, until, after I posted the message. In any case, want to Thank you for your time to reply.
      Asokan

      --- On Mon, 8/31/09, Frank Delaglio <delaglio@...> wrote:

      From: Frank Delaglio <delaglio@...>
      Subject: Re: [nmrpipe] Bruker Style Pseudo3D data processing macro
      To: nmrpipe@yahoogroups.com
      Date: Monday, August 31, 2009, 10:27 AM

       


      Ok ... I am no pulse program expert either, here's what I see ...

      The hint is that the outer loop of this pulse program
      indicates a count of 64 (i.e. number complex points you
      expect in your 15N dimension). AND, immediately inside of
      that loop is a 2 x loop with "igrad EA", which is the Echo-AntiEcho
      you expect for 15N in this case. SO ... its the Z-axis which is 15N.

      Here's a scheme I used on some related pseudo-3D data, maybe it's
      enough of a hint to help ... in your case, -zMODE will be Echo-AntiEcho,
      and you'll want to rename the planes to sort them in tau order ...

      bruk2pipe -in ./ser \
      -bad 0.0 -noaswap -DMX -decim 128 -dspfvs 12 -grpdly 0 \
      -xN 5120 -yN 16 -zN 32 \
      -xT 2499 -yT 16 -zT 16 \
      -xMODE DQD -yMODE Real -zMODE Complex \
      -xSW 1250.000 -ySW 16.000 -zSW 500.000 \
      -xOBS 500.134 -yOBS 1.000 -zOBS 500.130 \
      -xCAR 4.755 -yCAR 0.000 -zCAR 4.755 \
      -xLAB 1Hx -yLAB TAU -zLAB 1Hz \
      -ndim 3 -aq2D States \
      | nmrPipe -fn TP \
      | nmrPipe -fn ZTP \
      | nmrPipe -fn TP -hyper \
      | pipe2xyz -out ./fid/test%03d. fid -verb -ov

      > Dear All,
      > I've been using NMRpipe for several years without any problem. I
      > must Thank, Frank for this wonderful software and his service to
      > BIONMR community, and I'm a silent reader on this forum. Recently I
      > collected a CPMG based CT relaxation dispersion experiment using our
      > 800 Bruker AV with TCI cryoprobe. This data was collected as a
      > "pseudo3D" mode using  the pulse sequence "hsqcrexetf3gpsi3d" . The
      > cpmg field strength are given as in frequence units in "vdlist"
      > (0,50, 100, 200, 300, 400, 500, 600, 700,800) in random order. For
      > some strange reason, I'm unable to process the data correctly using
      > "NMRpipe". Here are some experimental parameters I used to set up
      > the expt.
      > F3: 1H (complex)
      > F2: 15N (Echo-Anticho) 128 TD points
      > F1: 10 in QF mode (10 corresponds to 10 CPMG field strength used in
      > the vdlist)
      > Total number of experiments 1280 (10 X 128).
      > Here is how  I converted the RAW data into NMRpipe format data.
      > #!/bin/csh
      >
      > bruk2pipe -in ./ser  \
      >   -bad 0.0 -noaswap -DMX -decim 12 -dspfvs 12 -grpdly -1  \
      >   -xN              2048  -yN               128  -zN                10  \
      >   -xT              1024  -yT                64  -zT                10  \
      >   -xMODE            DQD  -yMODE  Echo-AntiEcho  -zMODE           Real  \
      >   -xSW        12820.513  -ySW         3081.664  -zSW          500.000  \
      >   -xOBS         800.234  -yOBS          81.096  -zOBS          81.096  \
      >   -xCAR           4.773  -yCAR         118.092  -zCAR         118.092  \
      >   -xLAB             1Hx  -yLAB            15Ny  -zLAB            15Nz  \
      >   -ndim               3  -aq2D          States                         \
      >   -out ./fid/test%03d. fid -verb -ov
      >
      > I'm unable to successfully process the data using NMRpipe. If some
      > one of you have used the same pulse sequence and have successfully
      > processed the data using NMRpipe, could you please, share the
      > processing macro. I would appreciate any suggestion/help. Thank you
      > all for your time.
      >
      > Note: During data conversion, I got the following in the X-window. I
      > think this tells how the loops were executed in the pulse
      > program.I'm NOT a pulse program expert..
      > LOOP:                       lo to 6 times COUNTER (d21*vd*2 + 0.5)
      >
      > LOOP:                     lo to 7 times COUNTER (d21*vd*2 + 0.5)
      >
      > LOOP:                   lo to 3 times nbl    (nbl)
      >
      > LOOP:                 lo to 4 times ns     (ns)
      >
      > PHASE:              MCWRK  wr #0 if #0 zd igrad EA  MCWRK  ip5*2 
      > MCWRK  rpp3 rpp4 rpp5 rpp6 rpp7 rpp8 rpp9 rpp11 rpp31 (#5)
      > LOOP:               lo to LBLSTS1 times 2 (2)
      >
      > INCR:             MCWRK id10  MCWRK  ip6*2  MCWRK  ip11*2  MCWRK 
      > ip31*2 (1.622500e-04)
      > LOOP:             lo to LBLF1 times ST1CNT (64)
      >
      >
      >
      >
      >
      >
      >
      >


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