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

Re: [nmrpipe] Bruker processing woes

Expand Messages
  • Sarata Chandra Sahu
    Hi there, The acqsition mode in the 15N dimension could be different. Try the acquisition mode to be Echo-AntiEcho instead of States-TPPI and don t apply
    Message 1 of 3 , Nov 4, 2006
    • 0 Attachment
      Hi there,
      The acqsition mode in the 15N dimension could be different. Try the acquisition mode to be "Echo-AntiEcho" instead of "States-TPPI" and don't
      apply any phase correction in that axis.
      Good Luck!
      Sarata Sahu
      > Hi Everyone,
      >
      > I have a CBCACONH and HNCACB experiment taken on a bruker 800. When I
      > process them, they seem to look okay except for the phasing. I have peaks
      > that are out of phase with respect to the center of Nitrogen and Carbon.
      > I know this because when I correct peaks higher than the center value of
      > the spectrum, the other lower values become out of phase. Does anyone
      > know how to fix this? I listed my pulse sequences and processing
      > parameters below:
      >
      > HNCACB hncacbgpwg3d 3D sequence with inverse correlation for triple
      > resonance using multiple inept transfer steps F1(H) -> F3(N) -> F2(Ca ->
      > Cb,t1) -> F3(N,t2) -> F1(H,t3) on/off resonance Ca and C=O pulses using
      > shaped pulse phase sensitive (t1) phase sensitive (t2) using constant time
      > in t2 water suppression using watergate sequence
      >
      >
      > CBCACONH cbcaconhgpwg3d inverse correlation for triple resonance using
      > inept transfer steps F1(H) -> F2(Caliph.,t1 -> Ca) -> F2(C=O) -> F3(N,t2)
      > -> F1(H,t3) on/off resonance Ca and C=O pulses using shaped pulse phase
      > sensitive (t1) phase sensitive (t2) using constant time in t1 using constant
      > time in t2 water suppression using watergate sequence
      >
      > #!/bin/csh
      >
      > bruk2pipe -in ./ser -bad 0.0 -noaswap -DMX -decim 16 -dspfvs 12 -grpdly
      > -1 \ -xN 2048 -yN 96 -zN
      > 128 \ -xT 1024 -yT 48 -zT
      > 64 \ -xMODE DQD -yMODE States-TPPI -zMODE
      > States-TPPI \ -xSW 11160.714 -ySW 2920.561 -zSW
      > 15105.740 \ -xOBS 800.234 -yOBS 81.096 -zOBS
      > 201.226 \ -xCAR 4.658 -yCAR 117.965 -zCAR
      > 41.618 \ -xLAB 1H -yLAB 15N -zLAB
      > 13C \ -ndim 3 -aq2D States
      > \ -out ./fid/test%03d.fid -verb -ov
      >
      > sleep 5
      >
      > xyz2pipe -in ./fid/test%03d.fid -x \ | nmrPipe -fn
      > POLY -time \ #| nmrPipe -fn SP -off 0.50
      > -end 0.98 -c 0.5 -pow 2 \ | nmrPipe -fn SP -off 0.50 -end 0.98 -pow
      > 2 \ | nmrPipe -fn ZF -auto \ |
      > nmrPipe -fn FT -auto -verb \ | nmrPipe -fn EXT
      > -left -sw \ | nmrPipe -fn PS -p0 -161.2 -p1 0
      > -di \ | nmrPipe -fn TP
      > \ #| nmrPipe -fn LP -ps90-180 -pred 118 -verb \ | nmrPipe -fn
      > SP -off 0.50 -end 0.98 -pow 2 \ #| nmrPipe -fn SP -off 0.50
      > -end 0.98 -c 1.0 -pow 2 \ | nmrPipe -fn ZF -size auto
      > \ | nmrPipe -fn SIGN -i \ | nmrPipe -fn
      > FT -verb -auto \ | nmrPipe -fn PS -p0 30.2 -p1
      > -73.0 -di \ | nmrPipe -fn REV -sw
      > \ | pipe2xyz -out XY/xy%03d.DAT -ov -verb
      >
      > xyz2pipe -in XY/xy%03d.DAT -z -verb \ #| nmrPipe -fn LP
      > -ps90-180 -fb -pred 96 -after -verb \ | nmrPipe -fn SP -off 0.50
      > -end 0.98 -pow 2 \ #| nmrPipe -fn SP -off 0.50 -end 0.98 -c 1.0
      > -pow 2 \ | nmrPipe -fn ZF -auto \ | nmrPipe
      > -fn SIGN -i \ #| nmrPipe -fn FT -verb -inv
      > -alt \ | nmrPipe -fn FT -verb -auto
      > \ | nmrPipe -fn PS -p0 -14 -p1 8.4 -di \ | nmrPipe -fn
      > POLY -auto -ord 1 \ | pipe2xyz -out Z/z%03d.DAT -z -ov
      >
      >
      > xyz2pipe -in Z/z%03d.DAT -x \ | nmrPipe -fn POLY
      > -ord 1 -auto \ | nmrPipe -fn TP
      > \ | nmrPipe -fn POLY -ord 1 -auto \ | nmrPipe -fn TP
      > \ | nmrPipe -fn ZTP \ | pipe2xyz -out
      > Z/z%03d.DAT -ov -verb
      >
      > The only difference in the processing scheme for the two experiments is
      > the use of the reverse command--present in HNCACB, not in CBCACONH.
      >
      >
      >
      >
      >
      >
      > Yahoo! Groups Links
      >
      >
      >
      >


      --
      Sarata Chandra Sahu, Ph.D.
      Reasearch Biologist
      Department of Biological Sciences
      Carnegie Mellon University
      4400 Fifth Avenue
      Pittsburgh, PA 15213-2683
      E-Mail:scsahu@...
      Phone: (412)268-7338/3396 (O)
      (412)683-0444 (R)
      (412)478-4595 (Cell)
      Fax : (412)268-7083
    • andrewbenie
      Hi, I ve looked at both pulse sequences and you can only do States-TPPI or TPPI so don t try processing them as Echo/AntiEcho and you should not need to do any
      Message 2 of 3 , Nov 7, 2006
      • 0 Attachment
        Hi,
        I've looked at both pulse sequences and you can only do States-TPPI
        or TPPI so don't try processing them as Echo/AntiEcho and you should
        not need to do any phase correction in the indirect dimensions (except
        for maybe a 90 degree zero order phase shift. But that shouldn't be
        the case here) as the initial evolution delays are already compensated
        for. This means that if you need any phase correction (other than
        multiples of 90) there is most likely an error in your processing scheme.
        Normally for States-TPPI on Bruker you can simply set it in the
        conversion routine and use "FT -auto" later. What I noticed from your
        processing scheme is that you have the command "SIGN -i" which deletes
        the imaginaries. The FT of States-TPPI however needs the imaginaries,
        its absence would result in some interesting phases, which is what you
        see. Try removing the SIGN -i and reprocess. You may need to change
        States-TPPI to States-TPPI-N in the bruk2pipe conversion but as your
        processing scheme as it stands would work correctly for that kind of
        data (States-TPPI-N needs the negation of the imaginaries), I would
        simply try removing the SIGN command.
        Andy
      Your message has been successfully submitted and would be delivered to recipients shortly.