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IPAP Sequence Processing

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  • Nicole Brandon
    Hello, I am trying to get an IPAP sequence with gel signal suppression to work. Unfortunately, I have been running into problems with the processing, so I
    Message 1 of 4 , May 3, 2006
      Hello,

      I am trying to get an IPAP sequence with gel signal suppression to work.
      Unfortunately, I have been running into problems with the processing, so I can't
      optimize the pulse sequence. The pulse program was written (by another lab) for
      a Bruker spectrometer.

      The basic trouble seems to be with sorting and recombining the FIDs into an
      intelligible dataset. As I understand it, you run the experiment twice, once
      with l2=2 to get your antiphase and once with l2=1 to get your in-phase spectra.
      I don't really see why you need to further split (and recombine?) the datasets
      (since you have just acquired the two datasets separately), but if you process
      either one using a basic 2D processing scheme, you get unphase-able junk. I
      have also tried using the Bruker AU programs splitipap and splitipap2, which are
      supposed to separate interleaved data for Bruker-brand ipap sequences, but the
      result for this one isn't right. Lastly, I have tried using the COADD function
      in nmrPipe, but I seem to be using it incorrectly, since I still get a mess.

      I can't seem to attach my data to this post, but if you want to see it, send me
      an email and I'll send it to you as an attachment (about 3MB gzip'd and tar'd).

      Thanks for your help.

      Nicole Brandon
      Laboratory of Prof. Yan Xu
      University of Pittsburgh

      The relevant scripts are:
      #!/bin/csh

      bruk2pipe -in ./data/ser -bad 0.0 -noaswap -DMX \
      -decim 32 -dspfvs 12 -grpdly -1 \
      -xN 4096 -yN 256 \
      -xT 2048 -yT 128 \
      -xMODE DQD \
      -yMODE Complex \
      # -yMODE States-TPPI \
      -xSW 6009.615 -ySW 1460.707 \
      -xOBS 600.570 -yOBS 60.855 \
      -xCAR 4.752 -yCAR 115.987 \
      -xLAB HN -yLAB N \
      -ndim 2 -aq2D States \
      -out ./ipap_ip.fid -verb -ov

      set c = (1 0)

      foreach i (A B)
      nmrPipe -in ipap_ip.fid \
      | nmrPipe -fn COADD -cList $c -axis Y -time \
      | nmrPipe -fn MAC -macro $NMRTXT/bruk_ranceY.M -noRd -noWr \
      | nmrPipe -fn SOL \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      #| nmrPipe -fn FT -alt \
      | nmrPipe -fn PS -p0 92.8 -p1 0.0 -di \
      | nmrPipe -fn EXT -left -sw -verb \
      | nmrPipe -fn TP \
      -out $i.ft1 -verb -ov

      nmrPipe -in $i.ft1 \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      #| nmrPipe -fn FT -alt \
      | nmrPipe -fn PS -p0 0 -p1 0 -di \
      | nmrPipe -fn TP \
      #| nmrPipe -fn POLY -auto \
      -verb -ov -out $i.ft2

      set c = (0 1)
      end


      Pulseprogram:
      ;#include "Avance.incl"
      ;n15IPAP_nh.mam Collects 15N hsqc with splitting in 15N dimension
      ; as two spectra, one for each partner in the doublet.
      ; Signals from NH2 are suppressed.
      ;hsqcs3e.abx modified s3e version of N-H hsqc
      ;1 hn, 15n edited noesy to water protons
      ;history
      ;written by sg 2/23/93
      ;put in water flip_back 6/1/93
      ;change to waternh 7/29/93
      ;from Marcel Ottiger 11/18/97
      ;add NH filter 7/10/00
      ;trim unwanted 15N components 8/17/00

      ;#define PRESAT
      ;#define CARBON_LABEL

      ;p1 proton 90 at pl1, about 9u
      ;p2 1ms proton 90 at pl2 (long pulse selective for water)
      ;set phcor14 and phcor18!!!
      "p18=d1" ;presat at pl18

      ;p5=38 ;carbon pulse at dl2

      ;p7,p17 high power n15 90 on N
      ;p31 low power n15 90 (160ms) on N at pl31

      ;Define channel assignments:
      ;

      # include <Avance.incl>
      ;# include <Delay.incl>
      ;# include <Grad.incl>
      ;# include <Gradnt_new.incl>
      # include <bits_pitt.nt>

      ;#define H f1
      ;#define N f3
      ;#define C f2

      #ifdef CARBON_LABEL
      "d0=in0-4u-p5*2.0-p7*0.637" ;nitrogen incremental delay
      #else
      "d0=in0*0.5 - p7*0.637 - p1"
      #endif

      ;Gradient pulses
      "p20=2.5m" ;gp0=+50% or gp3=0%
      "p11=2.0m" ;gp1=-50%
      "p12=0.4m" ;gp4=+50% or gp3=0%
      "p13=0.6m" ;gp5=+50% or gp3=0%

      "d4=2.5m-p12" ;inept from 1H to 15N
      "d5=2.7m" ;inept from 1H to 15N
      "d11=5m"
      "d12=1m"
      "d24=p7*0.274"
      "d25=p1*2"
      "d26=p7-p1"

      1 ze
      10u ru2
      2 d11
      d12
      3 30u
      4 d12*3.0
      5 10u do:C
      10u do:N
      d12 LOCKH_ON
      10u pl5:C pl7:N
      #ifdef CARBON_LABEL
      10u fq1:C ;jump to 56ppm
      #endif
      ;***** presaturation *****
      #ifdef PRESAT
      10u pl18:H
      p18 ph1
      10u pl1:H
      #else
      d1
      #endif
      1m LOCKH_OFF
      10u pl1:H
      (p7 ph0):N ;eliminate Boltzmann
      ; p20:gp3
      ; 2m
      ;***** start 90-degree on h-n *****
      (p1 ph0):H
      2u
      p12:gp3
      d4
      (p7*2 ph6):N (d26 p1*2 ph0):H ;ph6n-cgc
      2u
      p12:gp3
      d4
      ;***** hsqc to nitrogen *****
      (p1 ph6):H
      2u
      p20:gp0 ;NOGRAD( 40, POSITIV, 50)
      3m pl1:H
      (p17 ph3):N
      ; if "l2==1" goto 20
      d5
      (p7*2 ph5):N (d26 p1*2 ph0):H
      d5
      d24 ; de-select -pei
      (p7 ph8):N (p1 ph4):H ;ph4h-cgc
      if "l2==2" goto 30
      d5
      (p7*2 ph5):N (d26 p1*2 ph0):H ;ph8h from ph0h-cgc
      d5
      d24
      (p7 ph9):N
      30 d0 pl5:C
      #ifdef CARBON_LABEL
      2u
      (p5*2 ph10):C ;(p1*2 ph0):H
      2u
      4u fq1:C ;jump to 177ppm
      (p5*2 ph10):C
      #else
      d25 ; (p1*2 ph0) no 180 for F1-coupled spectrum
      #endif
      d0
      if "l2==2" goto 40
      (p7 ph7):N
      goto 41
      40 (p7 ph17):N
      41 2u
      p11:gp1 ;GRAD( 41, NEGATIV, 40)
      2.0m pl1:H
      (p1 ph0)
      p13:gp5 ;GRAD( 50, POSITIV, 8.0)
      1100u pl2:H ;900u-cgc
      (p2 ph14)
      2u
      5u pl1:H
      (p1*2 ph15)
      2u
      5u pl2:H
      (p7*2 ph10):N (p2 ph14)
      2u
      p13:gp5 ;GRAD( 60, POSITIV, 8.0)
      1098u ph0 ;898u-cgc
      5u pl31:N
      go=2 ph31 cpd2:N
      d11 wr #0 if #0 zd
      d12 iu2
      lo to 3 times 2
      10u ru2
      10u dp7 ;nitrogens
      10u dp17
      lo to 4 times 2
      d12 id0
      d12 ip31
      d12 ip31
      lo to 5 times l3
      d12 do:C
      d12 do:N
      d12 LOCKH_ON
      exit

      ph0=0
      ph1=0
      ph3=0 0 2 2
      ph4=0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2
      ph5=0; 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
      ph6=1 3
      ph7=0 0 0 0 2 2 2 2
      ph17=1 1 1 1 3 3 3 3
      ph8=0 2 2 0
      ph9=1 3 3 1
      ph10=0
      ph14=2; adjusted -x hl2
      ph15=0
      ph31=0 2 2 0 2 0 0 2
    • mich
      Hello Nicole, I thick your pulse program is somewhat different from what you mentioned. In the pulseprogram, there is a line containing d12 iu2 Which will
      Message 2 of 4 , May 3, 2006
        Hello Nicole,
        I thick your pulse program is somewhat different from what you mentioned.
        In the pulseprogram, there is a line containing
        'd12 iu2'
        Which will increase the value of l2, and another line containing
        '10u ru2'
        Which will reset l2.
        So in fact, this pulse program is supposed to record both antiphase and in-
        phase spectra in 'ONE' experiment in each fid. In addition, TD in indirect
        dimension should be 2 (both in and anti phase) * 2 (quadrature detection) *
        l3.
        I hope this may help you solve the problem.

        Min-Kyu

        ++ ------------------------------------------- ++
        Min-Kyu Cho

        Doktorant student
        NMR based Structural Biology
        Max Planck Institute for Biophysical Chemistry
        Am Fassberg 11
        37077 Goettingen
        Germany
        Phone : +49 - 551 - 201 - 2221
        Fax : +49 - 551 - 201 - 2202
        -----Original Message-----
        From: nmrpipe@yahoogroups.com [mailto:nmrpipe@yahoogroups.com] On Behalf Of
        Nicole Brandon
        Sent: Wednesday, May 03, 2006 9:10 PM
        To: nmrpipe@yahoogroups.com
        Subject: [nmrpipe] IPAP Sequence Processing

        Hello,

        I am trying to get an IPAP sequence with gel signal suppression to work.
        Unfortunately, I have been running into problems with the processing, so I
        can't
        optimize the pulse sequence. The pulse program was written (by another
        lab) for
        a Bruker spectrometer.

        The basic trouble seems to be with sorting and recombining the FIDs into an
        intelligible dataset. As I understand it, you run the experiment twice,
        once
        with l2=2 to get your antiphase and once with l2=1 to get your in-phase
        spectra.
        I don't really see why you need to further split (and recombine?) the
        datasets
        (since you have just acquired the two datasets separately), but if you
        process
        either one using a basic 2D processing scheme, you get unphase-able junk. I
        have also tried using the Bruker AU programs splitipap and splitipap2,
        which are
        supposed to separate interleaved data for Bruker-brand ipap sequences, but
        the
        result for this one isn't right. Lastly, I have tried using the COADD
        function
        in nmrPipe, but I seem to be using it incorrectly, since I still get a mess.

        I can't seem to attach my data to this post, but if you want to see it,
        send me
        an email and I'll send it to you as an attachment (about 3MB gzip'd and
        tar'd).

        Thanks for your help.

        Nicole Brandon
        Laboratory of Prof. Yan Xu
        University of Pittsburgh

        The relevant scripts are:
        #!/bin/csh

        bruk2pipe -in ./data/ser -bad 0.0 -noaswap -DMX \
        -decim 32 -dspfvs 12 -grpdly -1 \
        -xN 4096 -yN 256 \
        -xT 2048 -yT 128 \
        -xMODE DQD \
        -yMODE Complex \
        # -yMODE States-TPPI \
        -xSW 6009.615 -ySW 1460.707 \
        -xOBS 600.570 -yOBS 60.855 \
        -xCAR 4.752 -yCAR 115.987 \
        -xLAB HN -yLAB N \
        -ndim 2 -aq2D States \
        -out ./ipap_ip.fid -verb -ov

        set c = (1 0)

        foreach i (A B)
        nmrPipe -in ipap_ip.fid \
        | nmrPipe -fn COADD -cList $c -axis Y -time \
        | nmrPipe -fn MAC -macro $NMRTXT/bruk_ranceY.M -noRd -noWr \
        | nmrPipe -fn SOL \
        | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT \
        #| nmrPipe -fn FT -alt \
        | nmrPipe -fn PS -p0 92.8 -p1 0.0 -di \
        | nmrPipe -fn EXT -left -sw -verb \
        | nmrPipe -fn TP \
        -out $i.ft1 -verb -ov

        nmrPipe -in $i.ft1 \
        | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT \
        #| nmrPipe -fn FT -alt \
        | nmrPipe -fn PS -p0 0 -p1 0 -di \
        | nmrPipe -fn TP \
        #| nmrPipe -fn POLY -auto \
        -verb -ov -out $i.ft2

        set c = (0 1)
        end


        Pulseprogram:
        ;#include "Avance.incl"
        ;n15IPAP_nh.mam Collects 15N hsqc with splitting in 15N dimension
        ; as two spectra, one for each partner in the doublet.
        ; Signals from NH2 are suppressed.
        ;hsqcs3e.abx modified s3e version of N-H hsqc
        ;1 hn, 15n edited noesy to water protons
        ;history
        ;written by sg 2/23/93
        ;put in water flip_back 6/1/93
        ;change to waternh 7/29/93
        ;from Marcel Ottiger 11/18/97
        ;add NH filter 7/10/00
        ;trim unwanted 15N components 8/17/00

        ;#define PRESAT
        ;#define CARBON_LABEL

        ;p1 proton 90 at pl1, about 9u
        ;p2 1ms proton 90 at pl2 (long pulse selective for water)
        ;set phcor14 and phcor18!!!
        "p18=d1" ;presat at pl18

        ;p5=38 ;carbon pulse at dl2

        ;p7,p17 high power n15 90 on N
        ;p31 low power n15 90 (160ms) on N at pl31

        ;Define channel assignments:
        ;

        # include <Avance.incl>
        ;# include <Delay.incl>
        ;# include <Grad.incl>
        ;# include <Gradnt_new.incl>
        # include <bits_pitt.nt>

        ;#define H f1
        ;#define N f3
        ;#define C f2

        #ifdef CARBON_LABEL
        "d0=in0-4u-p5*2.0-p7*0.637" ;nitrogen incremental delay
        #else
        "d0=in0*0.5 - p7*0.637 - p1"
        #endif

        ;Gradient pulses
        "p20=2.5m" ;gp0=+50% or gp3=0%
        "p11=2.0m" ;gp1=-50%
        "p12=0.4m" ;gp4=+50% or gp3=0%
        "p13=0.6m" ;gp5=+50% or gp3=0%

        "d4=2.5m-p12" ;inept from 1H to 15N
        "d5=2.7m" ;inept from 1H to 15N
        "d11=5m"
        "d12=1m"
        "d24=p7*0.274"
        "d25=p1*2"
        "d26=p7-p1"

        1 ze
        10u ru2
        2 d11
        d12
        3 30u
        4 d12*3.0
        5 10u do:C
        10u do:N
        d12 LOCKH_ON
        10u pl5:C pl7:N
        #ifdef CARBON_LABEL
        10u fq1:C ;jump to 56ppm
        #endif
        ;***** presaturation *****
        #ifdef PRESAT
        10u pl18:H
        p18 ph1
        10u pl1:H
        #else
        d1
        #endif
        1m LOCKH_OFF
        10u pl1:H
        (p7 ph0):N ;eliminate Boltzmann
        ; p20:gp3
        ; 2m
        ;***** start 90-degree on h-n *****
        (p1 ph0):H
        2u
        p12:gp3
        d4
        (p7*2 ph6):N (d26 p1*2 ph0):H ;ph6n-cgc
        2u
        p12:gp3
        d4
        ;***** hsqc to nitrogen *****
        (p1 ph6):H
        2u
        p20:gp0 ;NOGRAD( 40, POSITIV, 50)
        3m pl1:H
        (p17 ph3):N
        ; if "l2==1" goto 20
        d5
        (p7*2 ph5):N (d26 p1*2 ph0):H
        d5
        d24 ; de-select -pei
        (p7 ph8):N (p1 ph4):H ;ph4h-cgc
        if "l2==2" goto 30
        d5
        (p7*2 ph5):N (d26 p1*2 ph0):H ;ph8h from ph0h-cgc
        d5
        d24
        (p7 ph9):N
        30 d0 pl5:C
        #ifdef CARBON_LABEL
        2u
        (p5*2 ph10):C ;(p1*2 ph0):H
        2u
        4u fq1:C ;jump to 177ppm
        (p5*2 ph10):C
        #else
        d25 ; (p1*2 ph0) no 180 for F1-coupled spectrum
        #endif
        d0
        if "l2==2" goto 40
        (p7 ph7):N
        goto 41
        40 (p7 ph17):N
        41 2u
        p11:gp1 ;GRAD( 41, NEGATIV, 40)
        2.0m pl1:H
        (p1 ph0)
        p13:gp5 ;GRAD( 50, POSITIV, 8.0)
        1100u pl2:H ;900u-cgc
        (p2 ph14)
        2u
        5u pl1:H
        (p1*2 ph15)
        2u
        5u pl2:H
        (p7*2 ph10):N (p2 ph14)
        2u
        p13:gp5 ;GRAD( 60, POSITIV, 8.0)
        1098u ph0 ;898u-cgc
        5u pl31:N
        go=2 ph31 cpd2:N
        d11 wr #0 if #0 zd
        d12 iu2
        lo to 3 times 2
        10u ru2
        10u dp7 ;nitrogens
        10u dp17
        lo to 4 times 2
        d12 id0
        d12 ip31
        d12 ip31
        lo to 5 times l3
        d12 do:C
        d12 do:N
        d12 LOCKH_ON
        exit

        ph0=0
        ph1=0
        ph3=0 0 2 2
        ph4=0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2
        ph5=0; 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
        ph6=1 3
        ph7=0 0 0 0 2 2 2 2
        ph17=1 1 1 1 3 3 3 3
        ph8=0 2 2 0
        ph9=1 3 3 1
        ph10=0
        ph14=2; adjusted -x hl2
        ph15=0
        ph31=0 2 2 0 2 0 0 2







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      • overdone_us
        Hello Min-Kyu, I see what you mean; I see that I misunderstood those commands. I guess this experiment should always be run with l2=1, which is what I used in
        Message 3 of 4 , May 4, 2006
          Hello Min-Kyu,

          I see what you mean; I see that I misunderstood those commands. I
          guess this experiment should always be run with l2=1, which is what I
          used in one experiment that still doesn't process correctly. The
          experiments were run with TD(N)=4*l3 (i.e. I set l3=64), so for one
          experiment, both l2 & l3 were set correctly, and I still get garbage.

          Do you see any mistakes in the nmrPipe scheme?

          Thanks,
          Nicole

          --- In nmrpipe@yahoogroups.com, "mich" <mich@...> wrote:
          >
          > Hello Nicole,
          > I thick your pulse program is somewhat different from what you
          > mentioned. In the pulseprogram, there is a line containing
          > 'd12 iu2'
          > Which will increase the value of l2, and another line containing
          > '10u ru2'
          > Which will reset l2.
          > So in fact, this pulse program is supposed to record both antiphase
          > and in-phase spectra in 'ONE' experiment in each fid. In addition,
          > TD in indirect dimension should be 2 (both in and anti phase) * 2
          > (quadrature detection) * l3.
          > I hope this may help you solve the problem.
          >
          > Min-Kyu
          >
          > ++ ------------------------------------------- ++
          > Min-Kyu Cho
          >
          > Doktorant student
          > NMR based Structural Biology
          > Max Planck Institute for Biophysical Chemistry
          > Am Fassberg 11
          > 37077 Goettingen
          > Germany
          > Phone : +49 - 551 - 201 - 2221
          > Fax : +49 - 551 - 201 - 2202
          > -----Original Message-----
          > From: nmrpipe@yahoogroups.com [mailto:nmrpipe@yahoogroups.com] On
          Behalf Of
          > Nicole Brandon
          > Sent: Wednesday, May 03, 2006 9:10 PM
          > To: nmrpipe@yahoogroups.com
          > Subject: [nmrpipe] IPAP Sequence Processing
          >
          > Hello,
          >
          > I am trying to get an IPAP sequence with gel signal suppression to
          > work. Unfortunately, I have been running into problems with the
          > processing, so I can't optimize the pulse sequence. The pulse
          > program was written (by another lab) for a Bruker spectrometer.
          >
          > The basic trouble seems to be with sorting and recombining the FIDs
          > into an intelligible dataset. As I understand it, you run the
          > experiment twice, once with l2=2 to get your antiphase and once with
          > l2=1 to get your in-phase spectra.
          > I don't really see why you need to further split (and recombine?)
          > the datasets (since you have just acquired the two datasets
          > separately), but if you process either one using a basic 2D
          > processing scheme, you get unphase-able junk. I have also tried
          > using the Bruker AU programs splitipap and splitipap2, which are
          > supposed to separate interleaved data for Bruker-brand ipap
          > sequences, but the result for this one isn't right. Lastly, I have
          > tried using the COADD function in nmrPipe, but I seem to be using
          > it incorrectly, since I still get a mess.
          >
          > I can't seem to attach my data to this post, but if you want to see
          > it, send me an email and I'll send it to you as an attachment (about
          > 3MB gzip'd and tar'd).
          >
          > Thanks for your help.
          >
          > Nicole Brandon
          > Laboratory of Prof. Yan Xu
          > University of Pittsburgh
          >
          > The relevant scripts are:
          > #!/bin/csh
          >
          > bruk2pipe -in ./data/ser -bad 0.0 -noaswap -DMX \
          > -decim 32 -dspfvs 12 -grpdly -1 \
          > -xN 4096 -yN 256 \
          > -xT 2048 -yT 128 \
          > -xMODE DQD \
          > -yMODE Complex \
          > # -yMODE States-TPPI \
          > -xSW 6009.615 -ySW 1460.707 \
          > -xOBS 600.570 -yOBS 60.855 \
          > -xCAR 4.752 -yCAR 115.987 \
          > -xLAB HN -yLAB N \
          > -ndim 2 -aq2D States \
          > -out ./ipap_ip.fid -verb -ov
          >
          > set c = (1 0)
          >
          > foreach i (A B)
          > nmrPipe -in ipap_ip.fid \
          > | nmrPipe -fn COADD -cList $c -axis Y -time \
          > | nmrPipe -fn MAC -macro $NMRTXT/bruk_ranceY.M -noRd -noWr \
          > | nmrPipe -fn SOL \
          > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
          > | nmrPipe -fn ZF -auto \
          > | nmrPipe -fn FT \
          > #| nmrPipe -fn FT -alt \
          > | nmrPipe -fn PS -p0 92.8 -p1 0.0 -di \
          > | nmrPipe -fn EXT -left -sw -verb \
          > | nmrPipe -fn TP \
          > -out $i.ft1 -verb -ov
          >
          > nmrPipe -in $i.ft1 \
          > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
          > | nmrPipe -fn ZF -auto \
          > | nmrPipe -fn FT \
          > #| nmrPipe -fn FT -alt \
          > | nmrPipe -fn PS -p0 0 -p1 0 -di \
          > | nmrPipe -fn TP \
          > #| nmrPipe -fn POLY -auto \
          > -verb -ov -out $i.ft2
          >
          > set c = (0 1)
          > end
          >
          >
          > Pulseprogram:
          > ;#include "Avance.incl"
          > ;n15IPAP_nh.mam Collects 15N hsqc with splitting in 15N dimension
          > ; as two spectra, one for each partner in the doublet.
          > ; Signals from NH2 are suppressed.
          > ;hsqcs3e.abx modified s3e version of N-H hsqc
          > ;1 hn, 15n edited noesy to water protons
          > ;history
          > ;written by sg 2/23/93
          > ;put in water flip_back 6/1/93
          > ;change to waternh 7/29/93
          > ;from Marcel Ottiger 11/18/97
          > ;add NH filter 7/10/00
          > ;trim unwanted 15N components 8/17/00
          >
          > ;#define PRESAT
          > ;#define CARBON_LABEL
          >
          > ;p1 proton 90 at pl1, about 9u
          > ;p2 1ms proton 90 at pl2 (long pulse selective for water)
          > ;set phcor14 and phcor18!!!
          > "p18=d1" ;presat at pl18
          >
          > ;p5=38 ;carbon pulse at dl2
          >
          > ;p7,p17 high power n15 90 on N
          > ;p31 low power n15 90 (160ms) on N at pl31
          >
          > ;Define channel assignments:
          > ;
          >
          > # include <Avance.incl>
          > ;# include <Delay.incl>
          > ;# include <Grad.incl>
          > ;# include <Gradnt_new.incl>
          > # include <bits_pitt.nt>
          >
          > ;#define H f1
          > ;#define N f3
          > ;#define C f2
          >
          > #ifdef CARBON_LABEL
          > "d0=in0-4u-p5*2.0-p7*0.637" ;nitrogen incremental delay
          > #else
          > "d0=in0*0.5 - p7*0.637 - p1"
          > #endif
          >
          > ;Gradient pulses
          > "p20=2.5m" ;gp0=+50% or gp3=0%
          > "p11=2.0m" ;gp1=-50%
          > "p12=0.4m" ;gp4=+50% or gp3=0%
          > "p13=0.6m" ;gp5=+50% or gp3=0%
          >
          > "d4=2.5m-p12" ;inept from 1H to 15N
          > "d5=2.7m" ;inept from 1H to 15N
          > "d11=5m"
          > "d12=1m"
          > "d24=p7*0.274"
          > "d25=p1*2"
          > "d26=p7-p1"
          >
          > 1 ze
          > 10u ru2
          > 2 d11
          > d12
          > 3 30u
          > 4 d12*3.0
          > 5 10u do:C
          > 10u do:N
          > d12 LOCKH_ON
          > 10u pl5:C pl7:N
          > #ifdef CARBON_LABEL
          > 10u fq1:C ;jump to 56ppm
          > #endif
          > ;***** presaturation *****
          > #ifdef PRESAT
          > 10u pl18:H
          > p18 ph1
          > 10u pl1:H
          > #else
          > d1
          > #endif
          > 1m LOCKH_OFF
          > 10u pl1:H
          > (p7 ph0):N ;eliminate Boltzmann
          > ; p20:gp3
          > ; 2m
          > ;***** start 90-degree on h-n *****
          > (p1 ph0):H
          > 2u
          > p12:gp3
          > d4
          > (p7*2 ph6):N (d26 p1*2 ph0):H ;ph6n-cgc
          > 2u
          > p12:gp3
          > d4
          > ;***** hsqc to nitrogen *****
          > (p1 ph6):H
          > 2u
          > p20:gp0 ;NOGRAD( 40, POSITIV, 50)
          > 3m pl1:H
          > (p17 ph3):N
          > ; if "l2==1" goto 20
          > d5
          > (p7*2 ph5):N (d26 p1*2 ph0):H
          > d5
          > d24 ; de-select -pei
          > (p7 ph8):N (p1 ph4):H ;ph4h-cgc
          > if "l2==2" goto 30
          > d5
          > (p7*2 ph5):N (d26 p1*2 ph0):H ;ph8h from ph0h-cgc
          > d5
          > d24
          > (p7 ph9):N
          > 30 d0 pl5:C
          > #ifdef CARBON_LABEL
          > 2u
          > (p5*2 ph10):C ;(p1*2 ph0):H
          > 2u
          > 4u fq1:C ;jump to 177ppm
          > (p5*2 ph10):C
          > #else
          > d25 ; (p1*2 ph0) no 180 for F1-coupled spectrum
          > #endif
          > d0
          > if "l2==2" goto 40
          > (p7 ph7):N
          > goto 41
          > 40 (p7 ph17):N
          > 41 2u
          > p11:gp1 ;GRAD( 41, NEGATIV, 40)
          > 2.0m pl1:H
          > (p1 ph0)
          > p13:gp5 ;GRAD( 50, POSITIV, 8.0)
          > 1100u pl2:H ;900u-cgc
          > (p2 ph14)
          > 2u
          > 5u pl1:H
          > (p1*2 ph15)
          > 2u
          > 5u pl2:H
          > (p7*2 ph10):N (p2 ph14)
          > 2u
          > p13:gp5 ;GRAD( 60, POSITIV, 8.0)
          > 1098u ph0 ;898u-cgc
          > 5u pl31:N
          > go=2 ph31 cpd2:N
          > d11 wr #0 if #0 zd
          > d12 iu2
          > lo to 3 times 2
          > 10u ru2
          > 10u dp7 ;nitrogens
          > 10u dp17
          > lo to 4 times 2
          > d12 id0
          > d12 ip31
          > d12 ip31
          > lo to 5 times l3
          > d12 do:C
          > d12 do:N
          > d12 LOCKH_ON
          > exit
          >
          > ph0=0
          > ph1=0
          > ph3=0 0 2 2
          > ph4=0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2
          > ph5=0; 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
          > ph6=1 3
          > ph7=0 0 0 0 2 2 2 2
          > ph17=1 1 1 1 3 3 3 3
          > ph8=0 2 2 0
          > ph9=1 3 3 1
          > ph10=0
          > ph14=2; adjusted -x hl2
          > ph15=0
          > ph31=0 2 2 0 2 0 0 2
          >
          >
          >
          >
          >
          >
          >
          > Yahoo! Groups Links
          >
        • Min-Kyu Cho
          Dear Nicole, Could you check the value for variable c ? It should be (1 1.1) and (1 -1.1) to get IP+AP & IP-AP spectra. Regards, Min-Kyu == Min-Kyu Cho ==
          Message 4 of 4 , May 4, 2006
            Dear Nicole,
            Could you check the value for variable 'c'?
            It should be (1 1.1) and (1 -1.1) to get IP+AP & IP-AP spectra.

            Regards,
            Min-Kyu
            == Min-Kyu Cho
            == Ph.D. student
            == NMR based Structural Biology
            == Max-Planck Institute for Biophysical Chemistry
            == Goettingen, Germany
            == Tel	+49(551)201-2221
            == Fax	+49(551)201-2202
            


            overdone_us :
            Hello Min-Kyu,
            
            I see what you mean; I see that I misunderstood those commands.  I
            guess this experiment should always be run with l2=1, which is what I
            used in one experiment that still doesn't process correctly.  The
            experiments were run with TD(N)=4*l3 (i.e. I set l3=64), so for one
            experiment, both l2 & l3 were set correctly, and I still get garbage.
            
            Do you see any mistakes in the nmrPipe scheme?
            
            Thanks,
            Nicole
            
            --- In nmrpipe@yahoogroups.com, "mich" <mich@...> wrote:
              
            Hello Nicole,
            I thick your pulse program is somewhat different from what you 
            mentioned. In the pulseprogram, there is a line containing 
            	'd12 iu2'
            Which will increase the value of l2, and another line containing 
            	'10u ru2'
            Which will reset l2. 
            So in fact, this pulse program is supposed to record both antiphase
            and in-phase spectra in 'ONE' experiment in each fid. In addition, 
            TD in indirect dimension should be 2 (both in and anti phase) * 2 
            (quadrature detection) * l3.  
            I hope this may help you solve the problem.
            
            Min-Kyu
            
            ++ ------------------------------------------- ++
            Min-Kyu Cho
             
            Doktorant student
            NMR based Structural Biology 
            Max Planck Institute for Biophysical Chemistry
            Am Fassberg 11
            37077 Goettingen
            Germany
            Phone : +49 - 551 - 201 - 2221
            Fax     : +49 - 551 - 201 - 2202
            -----Original Message-----
            From: nmrpipe@yahoogroups.com [mailto:nmrpipe@yahoogroups.com] On
                
            Behalf Of
              
            Nicole Brandon
            Sent: Wednesday, May 03, 2006 9:10 PM
            To: nmrpipe@yahoogroups.com
            Subject: [nmrpipe] IPAP Sequence Processing
            
            Hello,
            
            I am trying to get an IPAP sequence with gel signal suppression to 
            work. Unfortunately, I have been running into problems with the 
            processing, so I can't optimize the pulse sequence.  The pulse 
            program was written (by another lab) for a Bruker spectrometer.
            
            The basic trouble seems to be with sorting and recombining the FIDs 
            into an intelligible dataset.  As I understand it, you run the 
            experiment twice, once with l2=2 to get your antiphase and once with 
            l2=1 to get your in-phase spectra.
              I don't really see why you need to further split (and recombine?) 
            the datasets (since you have just acquired the two datasets 
            separately), but if you process either one using a basic 2D 
            processing scheme, you get unphase-able junk.  I have also tried 
            using the Bruker AU programs splitipap and splitipap2, which are
            supposed to separate interleaved data for Bruker-brand ipap 
            sequences, but the result for this one isn't right.  Lastly, I have 
            tried using the COADD function in nmrPipe, but I seem to be using 
            it incorrectly, since I still get a mess.
            
            I can't seem to attach my data to this post, but if you want to see 
            it, send me an email and I'll send it to you as an attachment (about 
            3MB gzip'd and tar'd).
            
            Thanks for your help.
            
            Nicole Brandon
            Laboratory of Prof. Yan Xu
            University of Pittsburgh 
            
            The relevant scripts are:
            #!/bin/csh
            
            bruk2pipe -in ./data/ser -bad 0.0 -noaswap -DMX \
             -decim 32 -dspfvs 12  -grpdly -1  \
             -xN              4096  -yN               256  \
             -xT              2048  -yT               128  \
             -xMODE            DQD  \
             -yMODE        Complex  \
            # -yMODE    States-TPPI  \
             -xSW         6009.615  -ySW         1460.707  \
             -xOBS         600.570  -yOBS          60.855  \
             -xCAR           4.752  -yCAR         115.987  \
             -xLAB              HN  -yLAB               N  \
             -ndim               2  -aq2D          States  \
             -out ./ipap_ip.fid -verb -ov
            
            set c = (1 0)
            
            foreach i (A B)
            nmrPipe -in ipap_ip.fid \
            | nmrPipe  -fn COADD -cList $c -axis Y -time                \
            | nmrPipe  -fn MAC -macro $NMRTXT/bruk_ranceY.M -noRd -noWr \
            | nmrPipe  -fn SOL                                    \
            | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5    \
            | nmrPipe  -fn ZF -auto                               \
            | nmrPipe  -fn FT                                     \
            #| nmrPipe  -fn FT -alt                                \
            | nmrPipe  -fn PS -p0 92.8  -p1 0.0 -di               \
            | nmrPipe  -fn EXT -left -sw -verb                    \
            | nmrPipe  -fn TP                                     \
              -out $i.ft1 -verb -ov
            
            nmrPipe -in $i.ft1 \
            | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5    \
            | nmrPipe  -fn ZF -auto                               \
            | nmrPipe  -fn FT                                     \
            #| nmrPipe  -fn FT -alt                                \
            | nmrPipe  -fn PS -p0 0 -p1 0 -di                     \
            | nmrPipe  -fn TP                                     \
            #| nmrPipe  -fn POLY -auto                             \
               -verb -ov -out $i.ft2
            
            set c = (0 1)
            end
            
            
            Pulseprogram:
            ;#include "Avance.incl"
            ;n15IPAP_nh.mam Collects 15N hsqc with splitting in 15N dimension
            ;             as two spectra, one for each partner in the doublet.
            ;             Signals from NH2 are suppressed.
            ;hsqcs3e.abx   modified s3e version of N-H hsqc
            ;1 hn, 15n edited noesy to water protons
            ;history
            ;written by sg 2/23/93
            ;put in water flip_back 6/1/93
            ;change to waternh 7/29/93
            ;from Marcel Ottiger 11/18/97
            ;add NH filter 7/10/00
            ;trim unwanted 15N components 8/17/00
            
            ;#define PRESAT
            ;#define CARBON_LABEL
            
            ;p1	proton 90 at pl1, about 9u
            ;p2	1ms proton 90  at pl2 (long pulse selective for water)
            ;set phcor14 and phcor18!!!
            "p18=d1"	;presat at pl18
            
            ;p5=38          ;carbon pulse at dl2
            
            ;p7,p17	high power n15 90 on N
            ;p31	low power n15 90 (160ms) on N at pl31
            
            ;Define channel assignments:
            ;
            
            # include <Avance.incl>
            ;# include <Delay.incl>
            ;# include <Grad.incl>
            ;# include <Gradnt_new.incl>
            # include <bits_pitt.nt>
            
            ;#define H f1
            ;#define N f3
            ;#define C f2
            
            #ifdef CARBON_LABEL
            "d0=in0-4u-p5*2.0-p7*0.637"	;nitrogen incremental delay
            #else
            "d0=in0*0.5 - p7*0.637 - p1"
            #endif
            
            ;Gradient pulses
            "p20=2.5m"	;gp0=+50% or gp3=0%
            "p11=2.0m"	;gp1=-50%
            "p12=0.4m"	;gp4=+50%  or gp3=0%
            "p13=0.6m"	;gp5=+50%  or gp3=0%
            
            "d4=2.5m-p12"			;inept from 1H to 15N
            "d5=2.7m"			;inept from 1H to 15N
            "d11=5m"
            "d12=1m"
            "d24=p7*0.274"
            "d25=p1*2"
            "d26=p7-p1"
            
            1	ze
            	10u ru2
            2	d11
            	d12
            3	30u
            4	d12*3.0
            5	10u do:C
                    10u do:N
                    d12 LOCKH_ON
            	10u pl5:C pl7:N
            #ifdef CARBON_LABEL
            	10u fq1:C	;jump to 56ppm
            #endif
            ;*****	presaturation	*****
            #ifdef PRESAT
            	10u pl18:H
            	p18 ph1
            	10u pl1:H
            #else
            	d1
            #endif
            	1m LOCKH_OFF
            	10u pl1:H 
            	(p7 ph0):N         ;eliminate Boltzmann
            ;        p20:gp3
            ;	2m
            ;*****	start 90-degree on h-n	*****
            	(p1 ph0):H
            	2u
                    p12:gp3
            	d4
            	(p7*2 ph6):N (d26 p1*2 ph0):H  ;ph6n-cgc
            	2u
                    p12:gp3
            	d4
            ;*****	hsqc to nitrogen	*****
            	(p1 ph6):H
            	2u
                    p20:gp0		;NOGRAD( 40, POSITIV, 50)
            	3m pl1:H
            	(p17 ph3):N
            ;	if "l2==1" goto 20
            	d5
            	(p7*2 ph5):N (d26 p1*2 ph0):H
            	d5
                    d24   ; de-select -pei
            	(p7 ph8):N (p1 ph4):H ;ph4h-cgc
            	if "l2==2" goto 30
            	d5
            	(p7*2 ph5):N (d26 p1*2 ph0):H ;ph8h from ph0h-cgc
            	d5
                    d24
            	(p7 ph9):N
            30	d0 pl5:C
            #ifdef CARBON_LABEL
            	2u
            	(p5*2 ph10):C   ;(p1*2 ph0):H
            	2u
            	4u fq1:C 	;jump to 177ppm
            	(p5*2 ph10):C
            #else
             	d25  ;	(p1*2 ph0)   no 180 for F1-coupled spectrum
            #endif
            	d0
                    if "l2==2" goto 40
            	(p7 ph7):N
                    goto 41
            40      (p7 ph17):N
            41      2u
                    p11:gp1	;GRAD( 41, NEGATIV, 40)
            	2.0m pl1:H
            	(p1 ph0)
                    p13:gp5		;GRAD( 50, POSITIV, 8.0)
            	1100u pl2:H  ;900u-cgc
            	(p2 ph14)
            	2u
            	5u pl1:H
            	(p1*2 ph15)
            	2u
            	5u pl2:H
            	(p7*2 ph10):N (p2 ph14)
            	2u
                    p13:gp5		;GRAD( 60, POSITIV, 8.0)
            	1098u ph0  ;898u-cgc
                    5u pl31:N
            	go=2 ph31 cpd2:N
            	d11 wr #0 if #0 zd
            	d12 iu2
            lo to 3 times 2
            	10u ru2
            	10u dp7		;nitrogens
            	10u dp17
            lo to 4 times 2
            d12 id0
            d12 ip31
            d12 ip31
            lo to 5 times l3
            d12 do:C
            d12 do:N
            d12 LOCKH_ON
            exit
            
            ph0=0
            ph1=0
            ph3=0 0 2 2
            ph4=0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2
            ph5=0; 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
            ph6=1 3
            ph7=0 0 0 0 2 2 2 2
            ph17=1 1 1 1 3 3 3 3
            ph8=0 2 2 0
            ph9=1 3 3 1
            ph10=0
            ph14=2; adjusted -x hl2
            ph15=0
            ph31=0 2 2 0 2 0 0 2
            
            
            
            
            
            
             
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