Loading ...
Sorry, an error occurred while loading the content.

Re: [nmrpipe] Re: help me about hncacb and cbcacohn spetctrum' problem

Expand Messages
  • Sean Cahill
    Hi, it s interesting that the 13C SW does not match between the two experiments - we had a problem in xwinnmr that sometimes when a 3D experiment finished, it
    Message 1 of 8 , Apr 26, 2005
    • 0 Attachment
      Hi, it's interesting that the 13C SW does not match between the two
      experiments - we had a problem in xwinnmr that sometimes when a 3D
      experiment finished, it would update the acqu2s file with the wrong SW
      and if you use a processing script that reads it from the acqu2s file,
      the SW will be wrong. Check that the SW is the same for the acqu2 and
      acqu2s files (this can also be checked in xwinnmr by typing "2 sw" and
      comparing to "2s sw"). I hope this help, Sean

      Nicole Brandon wrote:
      >
      > On Tue, 26 Apr 2005 11:46:54 +0000, nmrpipe wrote
      > >
      > > There are 2 messages in this issue.
      > >
      > > Topics in this digest:
      > >
      > > 1. help me about hncacb and cbcacohn spetctrum' problem
      > > From: "ethernet3399" <ethernet3399@...>
      > > 2. RE: help me about hncacb and cbcacohn spetctrum' problem
      > > From: ±i¤¤¬ì <chungke@...>
      > >
      > > ________________________________________________________________________
      > ________________________________________________________________________
      > >
      > > Message: 1
      > > Date: Tue, 26 Apr 2005 02:23:01 -0000
      > > From: "ethernet3399" <ethernet3399@...>
      > > Subject: help me about hncacb and cbcacohn spetctrum' problem
      > >
      > > hi everybody!
      > > I am processing a protein's hncacb and cbcacohn spectrum. But I have
      > > some problem.
      > > referenced by a hsqc spectrum, I synchronize the three
      > > spectrums(hsqc,hncacb,cbcacohn), for the same peak in the hsqc(residue
      > > i), the CA(i-1) in the hncacb and the CA(i-1) in the cbcacohn's carbon
      > > chemical shift is different, CB(i-1)'s situation is same. And the
      > > difference(carbon chemical shift) is not all the same value for
      > > different residues. These two spectrums' process macro have little
      > > difference. I list them below.
      > >
      >
      > <snip>
      >
      > >
      > > The yN is different, for cbcacohn spectrum S/N is larger, so lowered
      > > that value for shorter time. Is that the reason?
      > >
      > > Thank you all!
      > >
      > > Tieying Zhang in shanghai China
      > > 2005,04,26
      > >
      > > ________________________________________________________________________
      > ________________________________________________________________________
      > >
      > > Message: 2
      > > Date: Tue, 26 Apr 2005 16:37:58 +0800
      > > From: ±i¤¤¬ì <chungke@...>
      > > Subject: RE: help me about hncacb and cbcacohn spetctrum' problem
      > >
      > > Hello Tieying,
      > >
      > > Is your protein partially deuterated? I seem to recall that
      > > deuteration would affect the spectral position of the carbons when one
      > > is trying to compare HNCACB with CBCA(CO)NH due to the differences in
      > > transfer pathway. On the other hand, HN(CO)CACB doesn't suffer from
      > > this problem (provided you can run it on your sample).
      > >
      > > Cheers,
      > >
      > > Chung-ke Chang
      > > Postdoctoral fellow
      > > Institute of Biomedical Sciences, Academia Sinica
      > > Nankang, Taipei, Taiwan
      > >
      >
      > <snip>
      >
      > Tieying,
      >
      > I am having the same trouble: the carbon (i-1) peaks are offset, even though the
      > proton and nitrogen shifts match up. Of course, I can force them to align by
      > offsetting one of the experiments, but I still need to know what the true
      > chemical shifts are. My protein is NOT deuterated, so that doesn't explain it.
      > What's curious is that I found a similar discrepancy when I processed the same
      > data via TopSpin and XwinNMR (Bruker). Do you notice the same problem when you
      > process your data in whatever Varian's processing software is?
      >
      > I suspect it is a referencing problem, because I have run this pair of
      > experiments before and my scripts worked. I'm also reasonably confident that I
      > set up the experiments correctly (again, I've done these before), but I suppose
      > anything is possible. In the pair of experiments that worked, I also had
      > different yN's (numbers of Nitrogen points) for the two experiments. So that is
      > not the cause. We reference our spectra to DSS.
      >
      > Unfortunately, I still haven't figured out the solution, so please post if you
      > know what we should try. I've attached my processing scripts (that work for one
      > set of data on one sample, but not the other set on a different sample). Yes,
      > the experiments were acquired on the same sample at the same temperature within
      > a couple days of each other (our sample is very stable). The sweep widths are
      > different on the carbon dimension due to a quirk of the CBCACONNH program I'm
      > using. That SHOULDN'T make a difference, but I'm retaking the data with
      > identical sw's just in case.
      >
      > I did notice one difference between our processing strategies, but that may be a
      > quirk of the pulse programs we used. I have to use the command REV -sw or else
      > my spectra is "upside down," due to the constant time portions of the pulse
      > sequences. I'm assuming your spectra are correctly oriented. We use different
      > baseline corrections, window functions (at least on 1H), and linear predictions
      > (or lack thereof), but those shouldn't make a big difference.
      >
      > Thank you for your time,
      >
      > Nicole Brandon
      > University of Pittsburgh
      >
      > CBCACONNH:
      > (conversion script)
      > #!/bin/csh
      >
      > bruk2pipe -in ./data/ser -bad 0.0 -noaswap -DMX -decim 16 -dspfvs 12 \
      > -xN 1024 -yN 62 -zN 128 \
      > -xT 512 -yT 31 -zT 64 \
      > -xMODE DQD -yMODE States-TPPI -zMODE States-TPPI \
      > -xSW 6009.615 -ySW 1337.793 -zSW 9657.170 \
      > -xOBS 600.030 -yOBS 60.801 -zOBS 150.878 \
      > -xCAR 4.690 -yCAR 116.010 -zCAR 42.656 \
      > -xLAB 1H -yLAB 15N -zLAB 13C \
      > -ndim 3 -aq2D States \
      > -out ./fid/cbcaconnh%03d.fid -verb -ov
      >
      > sleep 5
      >
      > # Set up using SR wrt DSS.
      > # SR(1H) = 7.19 Hz BF1 = 600.03 MHz O1 = 2821.60 Hz
      > # SR(15N) = -0.597 Hz BF1 = 60.800512 MHz O1 = 7052.859 Hz
      > # SR(13C) = -400.704 Hz BF1 = 150.877664 MHz O1 = 6035.107 Hz
      >
      > (processing script)
      > #!/bin/csh
      >
      > xyz2pipe -in fidSR/cbcaconnh%03d.fid -x -verb \
      > | nmrPipe -fn SOL \
      > | nmrPipe -fn GM -g1 10 -g2 15 -g3 0.1 -c 1.0 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -auto \
      > | nmrPipe -fn PS -p0 17.4 -p1 -77.8 -di \
      > | nmrPipe -fn EXT -x1 7.0ppm -xn 9.0ppm -sw \
      > #| nmrPipe -fn MED -nw 80 \
      > | nmrPipe -fn YTP \
      > | nmrPipe -fn LP -fb \
      > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -alt \
      > | nmrPipe -fn PS -p0 -178.2 -p1 0 -di \
      > | nmrPipe -fn REV -sw \
      > | nmrPipe -fn MED -nw 12 \
      > | nmrPipe -fn ZTP \
      > | nmrPipe -fn LP -fb \
      > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -alt \
      > | nmrPipe -fn PS -p0 165.9 -p1 7 -di \
      > | nmrPipe -fn REV -sw \
      > | nmrPipe -fn MED -nw 24 \
      > | pipe2xyz -out ftSR/cbcaconnh%03d.ft3 -y -verb
      >
      > # process order HNC, output order HCN
      > # HNC -> NHC -> CHN -> HCN
      >
      > HNCACB:
      > (conversion script)
      > #!/bin/csh
      >
      > bruk2pipe -in ./data/ser -bad 0.0 -noaswap -DMX -decim 16 -dspfvs 12 \
      > -xN 1024 -yN 44 -zN 128 \
      > -xT 512 -yT 22 -zT 64 \
      > -xMODE DQD -yMODE States-TPPI -zMODE States-TPPI \
      > -xSW 6009.615 -ySW 1337.793 -zSW 9053.871 \
      > -xOBS 600.030 -yOBS 60.801 -zOBS 150.878 \
      > -xCAR 4.689 -yCAR 116.011 -zCAR 42.657 \
      > -xLAB 1H -yLAB 15N -zLAB 13C \
      > -ndim 3 -aq2D States \
      > -out ./fid/hncacb%03d.fid -verb -ov
      >
      > sleep 5
      >
      > # Set up using SR wrt DSS.
      > # SR(1H) = 6.68 Hz BF1 = 600.03 MHz O1 = 2820.50 Hz
      > # SR(15N) = -0.648 Hz BF1 = 60.800512 MHz O1 = 7052.859 Hz
      > # SR(13C) = -400.829 Hz BF1 = 150.877664 MHz O1 = 6035.107 Hz
      >
      > (processing script)
      >
      > #!/bin/csh
      >
      > # HNCACB processing script
      >
      > xyz2pipe -in fid/hncacb%03d.fid -x -verb \
      > | nmrPipe -fn SOL \
      > | nmrPipe -fn GM -g1 6 -g2 12 -c 1.0 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT \
      > | nmrPipe -fn PS -p0 -159.0 -p1 -65.0 -di \
      > | nmrPipe -fn EXT -x1 7.0ppm -xn 9.0ppm -sw \
      > | nmrPipe -fn MED -nw 80 \
      > | nmrPipe -fn YTP \
      > | nmrPipe -fn LP -fb \
      > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -alt \
      > | nmrPipe -fn PS -p0 1.2 -p1 6.4 -di \
      > | nmrPipe -fn REV -sw \
      > | nmrPipe -fn MED -nw 12 \
      > | nmrPipe -fn ZTP \
      > | nmrPipe -fn LP -fb \
      > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -alt \
      > | nmrPipe -fn PS -p0 0 -p1 0 -di \
      > | nmrPipe -fn REV -sw \
      > | nmrPipe -fn MED -nw 24 \
      > | pipe2xyz -out ft/hncacb%03d.ft3 -y -verb
      >
      >
      >
      > Yahoo! Groups Links
      >
      >
      >
      >

      --
      ----------------------------------------------------
      Sean Cahill, Structural NMR Resource
      Albert Einstein College of Medicine
      1300 Morris Park Ave, Bronx, NY 10461
      Office: Ullmann-B8 E-mail: cahill@...
      Phone: (718) 430-2035
      http://www.yu.edu/aecomdb/facultydir/facultypage4.asp?id=477
    • Yufeng
      Hi Nicole, One possible reason for unmatched peaks in cbcaconh/hncacb is the mismatch of in20 vs in0 in cbcaconh for Bruker pp cbcaconhgp3d, which should be
      Message 2 of 8 , Apr 26, 2005
      • 0 Attachment
        Hi Nicole,

        One possible reason for unmatched peaks in cbcaconh/hncacb
        is the mismatch of in20 vs in0 in cbcaconh for Bruker pp cbcaconhgp3d,
        which should be same in values. Change of sw for C13 in eda
        will change in0 but not in20 so that the final pp is something
        between CT and semi-CT, or non-equal delayed sampling. You'll have
        to check the in20 manually to match it up with in0.

        Hope this helps.

        Yufeng



        ======= At 2005-04-26 22:41:29 you wrote =======

        >
        >
        >Tieying,
        >
        >I am having the same trouble: the carbon (i-1) peaks are offset, even though the
        >proton and nitrogen shifts match up. Of course, I can force them to align by
        >offsetting one of the experiments, but I still need to know what the true
        >chemical shifts are. My protein is NOT deuterated, so that doesn't explain it.
        > What's curious is that I found a similar discrepancy when I processed the same
        >data via TopSpin and XwinNMR (Bruker). Do you notice the same problem when you
        >process your data in whatever Varian's processing software is?
        >
        >I suspect it is a referencing problem, because I have run this pair of
        >experiments before and my scripts worked. I'm also reasonably confident that I
        >set up the experiments correctly (again, I've done these before), but I suppose
        >anything is possible. In the pair of experiments that worked, I also had
        >different yN's (numbers of Nitrogen points) for the two experiments. So that is
        >not the cause. We reference our spectra to DSS.
        >
        >Unfortunately, I still haven't figured out the solution, so please post if you
        >know what we should try. I've attached my processing scripts (that work for one
        >set of data on one sample, but not the other set on a different sample). Yes,
        >the experiments were acquired on the same sample at the same temperature within
        >a couple days of each other (our sample is very stable). The sweep widths are
        >different on the carbon dimension due to a quirk of the CBCACONNH program I'm
        >using. That SHOULDN'T make a difference, but I'm retaking the data with
        >identical sw's just in case.
        >
        >I did notice one difference between our processing strategies, but that may be a
        >quirk of the pulse programs we used. I have to use the command REV -sw or else
        >my spectra is "upside down," due to the constant time portions of the pulse
        >sequences. I'm assuming your spectra are correctly oriented. We use different
        >baseline corrections, window functions (at least on 1H), and linear predictions
        >(or lack thereof), but those shouldn't make a big difference.
        >
        >Thank you for your time,
        >
        >Nicole Brandon
        >University of Pittsburgh
        >

        = = = = = = = = = = = = = = = = = = = =


        Yufeng Tong
        Dept. Physiol. & Biophys.
        Case Western Reserve Univ.
        Cleveland, Ohio 44106
        Tel: (216)368-8654 (O)
        _______________________________________________________________________
        Help Zhu Ling at http://www.helpzhuling.org
      • ethernet3399
        Hi Delaglio, Thanks a lot! I have tried your suggestion, and it works! I appreciate your help! For the phase corrections, I will follow your reminder, thank
        Message 3 of 8 , Apr 26, 2005
        • 0 Attachment
          Hi Delaglio,
          Thanks a lot! I have tried your suggestion, and it works! I appreciate
          your help!

          For the phase corrections, I will follow your reminder, thank you very
          much!

          Tieying Zhang
          2005,04,27

          --- In nmrpipe@yahoogroups.com, Frank Delaglio <delaglio@s...> wrote:
          >
          > Greetings,
          >
          > It's not unusual for the (CO) versions of experiments to have
          > imaginary data with inverted sign, which means that the 13C
          > dimension will be reversed. Use "FT -neg" in this case.
          >
          > Also, note there some non-ideal phase corrections, such as:
          >
          > > | nmrPipe -fn PS -p0 47.0 -p1 -107.0 -di
          >
          > Just a reminder, this is bad news, and should be avoided when
          > possible, otherwise:
          >
          > 1. There will be a curved baseline distortion.
          >
          > 2. Folded peaks will have distorted phase.
          >
          > 3. It will not be possible to reconstruct imaginary data perfectly
          > after they are deleted.
          >
          > Delays should be carefully adjusted and balanced so that P1 is either:
          >
          > Delay: 0 point P1 = 0 FID: 1st point scale -c 0.5
          >
          > Delay: 1/2 point P1 = 180 FID: 1st point Scale -c 1.0
          > Spectrum: Folded peaks have
          opposite sign
          >
          > Delay: 1 point P1 = 360 FID: 1st point scale -c 1.0
          > Spectrum: Use "POLY -auto -ord 0"
          >
          > On
          > Tue, 26 Apr 2005, ethernet3399 wrote:
          >
          > >
          > >
          > >
          > > hi everybody!
          > > I am processing a protein's hncacb and cbcacohn spectrum. But I have
          > > some problem.
          > > referenced by a hsqc spectrum, I synchronize the three
          > > spectrums(hsqc,hncacb,cbcacohn), for the same peak in the hsqc(residue
          > > i), the CA(i-1) in the hncacb and the CA(i-1) in the cbcacohn's carbon
          > > chemical shift is different, CB(i-1)'s situation is same. And the
          > > difference(carbon chemical shift) is not all the same value for
          > > different residues. These two spectrums' process macro have little
          > > difference. I list them below.
          > >
          > > the cbcacohn:
          > > #!/bin/csh -f
          > > #
          > > #
          > > # nmrpipe script for processing 3D CBCA(CO)NH
          > > #
          > > #
          > >
          > > set CONVERSION = y
          > > set PHASECORRECTION = n
          > > set PROCESSING = y
          > > set PIPE2UCSF = y
          > > set PIPE2NV = n
          > > set PIPE = /usr/local/NMRPipe/nmrtxt
          > >
          > > set fidin=fid
          > > set wdir=/home/chang/nmrdata/ubl3/UBL3-20050425-gcbca-co-nh.fid
          > >
          > > set fucsf=$wdir/Processed/UBL3-20050425-gcbca-co-nh.ucsf
          > > set fnv=$wdir/Processed
          > >
          > > ##################################################
          > > #####################
          > > #1. data conversion
          > >
          > > if ($CONVERSION == 'y') then
          > > var2pipe -verb -in fid -aqORD 1
          > > \
          > > -xN 1024 -yN 92 -zN 64
          > > \
          > > -xT 512 -yT 46 -zT 32
          > > \
          > > -xMODE Complex -yMODE Complex -zMODE Complex
          > > \
          > > -xSW 10000 -ySW 8445 -zSW 1960
          > > \
          > > -xOBS 599.660 -yOBS 150.86 -zOBS 60.77
          > > \
          > > -xCAR 4.76222 -yCAR 45.987 -zCAR 115.73
          > > \
          > > -xLAB HN -yLAB CAB -zLAB N
          > > \
          > > -ndim 3
          > > \
          > > | nmrPipe -fn MAC -macro $PIPE/ranceZ.M -noRd -noWr \
          > > | pipe2xyz -out $wdir/Processed/tmp-fid/tmp%03d.fid -x -ov -verb
          > >
          > > echo '+++CONVERSION DONE+++'
          > >
          > > endif
          > >
          > > ##################################################
          > > #####################
          > > # 2. phase correction
          > >
          > > if ($PHASECORRECTION == 'y') then
          > >
          > > nmrPipe -in $wdir/Processed/tmp-fid/tmp001.fid -verb \
          > > | nmrPipe -fn ZF -size 512
          > > \
          > > | nmrPipe -fn GMB -c 0.5 -lb -5.0 -gb 0.01
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 -94 -p1 0.0 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > | nmrPipe -fn TP
          > > \
          > > | nmrPipe -fn SP -off 0.5
          > > \
          > > | nmrPipe -fn ZF -size 256
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > -out tmp001.ft2 -verb -ov
          > > exit
          > > xyz2pipe -in plane%03d.ft12 -z
          > > \
          > > | nmrPipe -fn ZF -size 128
          > > \
          > > | nmrPipe -fn SP -off 0.5
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 47.0 -p1 -107.0 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > | pipe2xyz -ov -verb -out plane%03d.spec -z -inPlace
          > >
          > > echo '+++PROCESSING DONE+++'
          > >
          > > endif
          > >
          > > #exit
          > >
          > > ##################################################
          > > ######################
          > > # 3. processing
          > >
          > > if ($PROCESSING == 'y') then
          > >
          > >
          > >
          > > xyz2pipe -in $wdir/Processed/tmp-fid/tmp%03d.fid -x
          > > \
          > > | nmrPipe -fn ZF -size 2048
          > > \
          > > | nmrPipe -fn SP -off 0.5 -pow 2.0
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 143 -p1 59 -di
          > > \
          > > | nmrPipe -fn EXT -x1 11ppm -xn 6.0ppm -sw
          > > \
          > > | nmrPipe -fn TP
          > > \
          > > | nmrPipe -fn ZF -size 256
          > > \
          > > | nmrPipe -fn SP -off 0.5 -pow 2.0
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 -66.2 -p1 126 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > | pipe2xyz -ov -verb -out $wdir/Processed/FT2/cbcaconh%03d.ft2
          > > -y
          > >
          > > xyz2pipe -in $wdir/Processed/FT2/cbcaconh%03d.ft2 -z
          > > \
          > > | nmrPipe -fn ZF -size 256
          > > \
          > > | nmrPipe -fn SP -off 0.5 -pow 2.0
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 0 -p1 0.0 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > | pipe2xyz -ov -verb -out $wdir/Processed/FT3/cbcaconh%03d.ft3 -z
          > > -inPlace
          > >
          > > echo '+++PROCESSING DONE+++'
          > >
          > > endif
          > >
          > > ##################################################
          > > ######################
          > > # 4. format conversion
          > >
          > > if ($PIPE2UCSF == 'y') then
          > >
          > > echo '+++pipe2ucsf+++'
          > >
          > > xyz2pipe -verb -in $wdir/Processed/FT3/cbcaconh%03d.ft3 -x >
          > > temp.ft3
          > > pipe2ucsf temp.ft3 $fucsf
          > >
          > > rm temp.ft3
          > >
          > > endif
          > >
          > > if ($PIPE2NV == 'y') then
          > >
          > > echo '+++pipe2nv+++'
          > >
          > > xyz2pipe -verb -in $wdir/Processed/FT3/cbcaconh%03d.ft3 -x \
          > > |pipe2xyz -out UBL3-20050425-gcbca-co-nh.nv -nv -ov -verb -to 0
          > >
          > > cp UBL3-20050425-gcbca-co-nh.nv $fnv
          > > rm UBL3-20050425-gcbca-co-nh.nv
          > >
          > > endif
          > >
          > > exit
          > >
          > >
          > > the hncacb:
          > > #!/bin/csh -f
          > > #
          > > #
          > > # nmrpipe script for processing 3D HNCACB
          > > #
          > > #
          > >
          > > set CONVERSION = y
          > > set PHASECORRECTION = n
          > > set PROCESSING = y
          > > set PIPE2UCSF = y
          > > set PIPE2NV = n
          > > set PIPE = /usr/local/NMRPipe/nmrtxt
          > >
          > > set fidin=fid
          > > set wdir=/home/chang/nmrdata/ubl3/UBL3-20050418-ghncacb.fid
          > >
          > > set fucsf=$wdir/Processed/UBL3-20050418-ghncacb.ucsf
          > > set fnv=$wdir/Processed
          > >
          > > ##################################################
          > > #####################
          > > #1. data conversion
          > >
          > > if ($CONVERSION == 'y') then
          > > var2pipe -verb -in fid -aqORD 1
          > > \
          > > -xN 1024 -yN 128 -zN 64 \
          > > -xT 512 -yT 64 -zT 32 \
          > > -xMODE Complex -yMODE Complex -zMODE Complex
          > > \
          > > -xSW 10000 -ySW 8445 -zSW 1960
          > > \
          > > -xOBS 599.660 -yOBS 150.86 -zOBS 60.77
          > > \
          > > -xCAR 4.76256 -yCAR 45.987 -zCAR 115.73
          > > \
          > > -xLAB HN -yLAB CAB -zLAB N
          > > \
          > > -ndim 3
          > > \
          > > | nmrPipe -fn MAC -macro $PIPE/ranceZ.M -noRd -noWr \
          > > | pipe2xyz -out $wdir/Processed/tmp-fid/tmp%03d.fid -x -ov -verb
          > >
          > > echo '+++CONVERSION DONE+++'
          > >
          > > endif
          > >
          > > ##################################################
          > > #####################
          > > # 2. phase correction
          > >
          > > if ($PHASECORRECTION == 'y') then
          > >
          > > nmrPipe -in $wdir/Processed/tmp-fid/tmp001.fid -verb \
          > > | nmrPipe -fn ZF -size 512
          > > \
          > > | nmrPipe -fn GMB -c 0.5 -lb -5.0 -gb 0.01
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 -94 -p1 0.0 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > | nmrPipe -fn TP
          > > \
          > > | nmrPipe -fn SP -off 0.5
          > > \
          > > | nmrPipe -fn ZF -size 256
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > -out tmp001.ft2 -verb -ov
          > > exit
          > > xyz2pipe -in plane%03d.ft12 -z
          > > \
          > > | nmrPipe -fn ZF -size 128
          > > \
          > > | nmrPipe -fn SP -off 0.5
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 47.0 -p1 -107.0 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > | pipe2xyz -ov -verb -out plane%03d.spec -z -inPlace
          > >
          > > echo '+++PROCESSING DONE+++'
          > >
          > > endif
          > >
          > > #exit
          > >
          > > ##################################################
          > > ######################
          > > # 3. processing
          > >
          > > if ($PROCESSING == 'y') then
          > >
          > >
          > >
          > > xyz2pipe -in $wdir/Processed/tmp-fid/tmp%03d.fid -x
          > > \
          > > | nmrPipe -fn ZF -size 2048
          > > \
          > > | nmrPipe -fn SP -off 0.5 -pow 2.0
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 -79 -p1 -60 -di
          > > \
          > > | nmrPipe -fn EXT -x1 11ppm -xn 6.0ppm -sw
          > > \
          > > | nmrPipe -fn TP
          > > \
          > > | nmrPipe -fn ZF -size 256
          > > \
          > > | nmrPipe -fn SP -off 0.5 -pow 2.0
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 473 -p1 146 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > | pipe2xyz -ov -verb -out $wdir/Processed/FT2/cbcanh%03d.ft2 -y
          > >
          > > xyz2pipe -in $wdir/Processed/FT2/cbcanh%03d.ft2 -z
          > > \
          > > | nmrPipe -fn ZF -size 256
          > > \
          > > | nmrPipe -fn SP -off 0.5 -pow 2.0
          > > \
          > > | nmrPipe -fn FT
          > > \
          > > | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di
          > > \
          > > | nmrPipe -fn POLY -auto -ord 1
          > > \
          > > | pipe2xyz -ov -verb -out $wdir/Processed/FT3/cbcanh%03d.ft3 -z
          > > -inPlace
          > >
          > > echo '+++PROCESSING DONE+++'
          > >
          > > endif
          > >
          > > ##################################################
          > > ######################
          > > # 4. format conversion
          > >
          > > if ($PIPE2UCSF == 'y') then
          > >
          > > echo '+++pipe2ucsf+++'
          > >
          > > xyz2pipe -verb -in $wdir/Processed/FT3/cbcanh%03d.ft3 -x >
          > > temp.ft3
          > > pipe2ucsf temp.ft3 $fucsf
          > >
          > > rm temp.ft3
          > >
          > > endif
          > >
          > > if ($PIPE2NV == 'y') then
          > >
          > > echo '+++pipe2nv+++'
          > >
          > > xyz2pipe -verb -in $wdir/Processed/FT3/cbcanh%03d.ft3 -x \
          > > |pipe2xyz -out UBL3-20050418-ghncacb.nv -nv -ov -verb -to 0
          > >
          > > cp UBL3-20050418-ghncacb.nv $fnv
          > > rm UBL3-20050418-ghncacb.nv
          > >
          > > endif
          > >
          > > exit
          > >
          > >
          > > The yN is different, for cbcacohn spectrum S/N is larger, so lowered
          > > that value for shorter time. Is that the reason?
          > >
          > > Thank you all!
          > >
          > > Tieying Zhang in shanghai China
          > > 2005,04,26
          > >
          > >
          > >
          > >
          > >
          > >
          > >
          > >
          > >
          > >
          > > Yahoo! Groups Links
          > >
          > >
          > >
          > >
          > >
          > >
          > >
          > >
        • Nicole Brandon
          Thank you to everyone who replied. The pulse sequence I m using is Bruker s cbcaconhgpwg3d. I discovered that CNST23 = O2p. I had adjusted the o2p without
          Message 4 of 8 , Apr 27, 2005
          • 0 Attachment
            Thank you to everyone who replied. The pulse sequence I'm using is Bruker's
            cbcaconhgpwg3d. I discovered that CNST23 = O2p. I had adjusted the o2p without
            updating cnst23, thus I was using the wrong value for zCAR in my bruker2pipe
            script. So I suppose the moral is: read the comments to the pulse sequence
            every time you set up an experiment, even if you've used this experiment before.

            Thanks again for your help.

            Nicole Brandon
            University of Pittsburgh

            PS If you want to try to use my CBCACONNH script for your data, you need to take
            out the REV -sw on the carbon dimension. I was playing around with that and
            forgot to take it out when I copy/pasted into my previous post.
          Your message has been successfully submitted and would be delivered to recipients shortly.