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processing new varian 3-D data

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  • Jessica L. Dion
    Hello - We ve recently been running a few of Varian s protein pack pulse sequences, and I ve had terrible luck processing the resulting data with nmrPipe.
    Message 1 of 2 , Apr 12, 1999
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      Hello -

      We've recently been running a few of Varian's "protein pack" pulse
      sequences, and I've had terrible luck processing the resulting data with
      nmrPipe. The data looks fine processed with Vnmr. Normally, data
      processed with nmrPipe looks better (in my opinion) than vnmr data, but
      this is not the case here.

      I figured out that when we run some of the 3-D experiments as 2-D
      experiments (for optimization purposes), the 2-D experiments need to be
      gradsorted for nmrPipe to process them correctly, even though vnmr itself
      doesn't need the data to be gradsorted.

      The corresponding 3-D data sets are giving me all kinds of grief. I am
      seeing some strange symmetry related problems - not a mirroring exactly,
      but definitely a duplication of sorts. Of course, this prevents me from
      phasing in a meaningful way also.

      If any of you have had luck processing the data from some of the newer 3-D
      experiments, or have any tips on troubleshooting processing scripts with
      this strange data, I'm all ears.

      Thank you!

      - Jessica Dion
      Biochemistry Dept.
      University of Vermont
    • Banville Debra DL
      Jessica, I am pasting some of my notes on 3D conversion/processing below w/ one example a protein pack expt, the hncacb, conversion and processing .com files.
      Message 2 of 2 , Apr 12, 1999
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        Jessica,
        I am pasting some of my notes on 3D conversion/processing below w/ one
        example a protein pack expt, the hncacb, conversion and processing .com
        files. Hope this helps in deciphering the data:
        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
        +
        VARIAN DATA CONVERSION
        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
        +
        >vi propar (or use the varian conversion w/in nmrDraw menu to get the
        relevant parameters read into a fid.com file)
        Parameters needed are:
        sfrq, dfrq, dfrq2, np, ni, ni2, sw, sw1, sw2, array

        Some parameters to consider for the data conversion (fid.com),
        >Sensitivity Enhancement (SE or PEP) along z-axis:
        | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr \
        |pipe2xyz -out fidc/hnca%03d.fid -verb -ov -to 0

        >Acquisition Order:
        -acq ORD 0 [default] if array='phase2,phase'
        -acq ORD 1 if array='phase,phase2'

        Some parameters to consider for the data processing (ft3.com),

        xyz2pipe -in pdata/ft3d%03d.ft1 -z -verb \
        etc...
        | nmrPipe -fn SIGN -i \ if f1coef='1 0 0 0 0 0 1 0' e.g. ghn_cacb
        is needed on the instrument.
        --------------------------------------------------
        EXAMPLE#1-Protein Pack ghn_cacb.com
        -------------------start of ghncacb_fid.com-----------------------------
        #!/bin/csh

        # Varian 3D States-Mode Standard Protein Pack ghncacb Conversion:
        # Sensitivity Enhanced along N15 dimension (Z-axis) => ranceZ.M
        # Collected on a Unity Inova w/ Digital Processing (dsp).

        zcat ./fid.Z | var2pipe \
        -xN 1152 -yN 100 -zN 64 \
        -xT 576 -yT 50 -zT 32 \
        -xMODE Complex -yMODE Complex -zMODE Complex \
        -xSW 8003.20 -ySW 9050.00 -zSW 1400.02 \
        -xOBS 500.0453224 -yOBS 125.7413607 -zOBS 50.6747054 \
        -xCAR 4.78 -yCAR 46.08 -zCAR 115.54 \
        -xLAB HN -yLAB CaCb -zLAB N \
        -ndim 3 -aq2D States -aqORD 1 \
        | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr \
        |pipe2xyz -out fidc/hncacb%03d.fid -verb -ov -to 0

        echo DONE.
        -------------------end of ghncacb_fid.com-----------------------------

        -------------------start of ghncacb_ft3.com-----------------------------
        #!/bin/csh

        echo "FT in F3"

        xyz2pipe -in fidc/hncacb%03d.fid -x -verb \
        | nmrPipe -fn SOL \
        | nmrPipe -fn SP -off 0.35 -end 0.95 -pow 2 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT -auto \
        | nmrPipe -fn PS -p0 110.0 -p1 0.0 -di \
        | nmrPipe -fn EXT -left -sw \
        | pipe2xyz -out pdata/ft3d%03d.ft1 -x

        echo "preliminary FT in F1"

        xyz2pipe -in pdata/ft3d%03d.ft1 -z \
        | nmrPipe -fn SP -off 0.4 -end 0.95 -pow 2 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT -auto \
        | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \
        | pipe2xyz -out pdata/ft3d%03d.ft1 -z -inPlace

        echo "FT in F2"
        echo ">with forward LP and SIGN -i reversal in F2"

        xyz2pipe -in pdata/ft3d%03d.ft1 -y \
        | nmrPipe -fn LP -ps0-0 \
        | nmrPipe -fn SIGN -i \
        | nmrPipe -fn SP -off 0.35 -end 1 -pow 2 -c 1.0 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT -auto \
        | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \
        | pipe2xyz -out pdata/ft3d%03d.ft1 -y -inPlace

        echo "final FT in F1"
        echo ">with forward back LP"

        xyz2pipe -in pdata/ft3d%03d.ft1 -z -verb \
        | nmrPipe -fn HT -auto \
        | nmrPipe -fn PS -p0 0.0 -p1 0.0 -inv \
        | nmrPipe -fn FT -inv \
        | nmrPipe -fn ZF -inv \
        | nmrPipe -fn SP -off 0.4 -end 0.95 -pow 2 -c 0.5 -inv \
        | nmrPipe -fn LP -fb \
        | nmrPipe -fn SP -off 0.44 -end 0.95 -pow 2 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT -auto \
        | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \
        | pipe2xyz -out pdata/hncacb%03d.dat -z


        echo DONE!

        /bin/rm pdata/ft3d*.ft1
        -------------------end of ghncacb_ft3.com-----------------------------

        Debbie

        ++++++++++++++++++++++++++++++++++++++++++++++
        Debra.Banville@...
        tel: 302-886-8082; fax: 302-886-5382
        office: NLW3035; lab: NLW3043
        snail mail: Zeneca Pharmaceuticals
        1800 Concord Pike, PO Box#15437
        Wilmington, Delaware 19850-5437
        ++++++++++++++++++++++++++++++++++++++++++++++

        > ----------
        > From: Jessica L. Dion[SMTP:jdion@...]
        > Sent: Monday, April 12, 1999 1:56 PM
        > To: nmrpipe@onelist.com
        > Subject: [nmrpipe] processing new varian 3-D data
        >
        > From: "Jessica L. Dion" <jdion@...>
        >
        >
        > Hello -
        >
        > We've recently been running a few of Varian's "protein pack" pulse
        > sequences, and I've had terrible luck processing the resulting data with
        > nmrPipe. The data looks fine processed with Vnmr. Normally, data
        > processed with nmrPipe looks better (in my opinion) than vnmr data, but
        > this is not the case here.
        >
        > I figured out that when we run some of the 3-D experiments as 2-D
        > experiments (for optimization purposes), the 2-D experiments need to be
        > gradsorted for nmrPipe to process them correctly, even though vnmr itself
        > doesn't need the data to be gradsorted.
        >
        > The corresponding 3-D data sets are giving me all kinds of grief. I am
        > seeing some strange symmetry related problems - not a mirroring exactly,
        > but definitely a duplication of sorts. Of course, this prevents me from
        > phasing in a meaningful way also.
        >
        > If any of you have had luck processing the data from some of the newer 3-D
        > experiments, or have any tips on troubleshooting processing scripts with
        > this strange data, I'm all ears.
        >
        > Thank you!
        >
        > - Jessica Dion
        > Biochemistry Dept.
        > University of Vermont
        >
        >
        > ------------------------------------------------------------------------
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