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CBCACONH conversion problem to NMRpipe formate

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  • Hussan, Syed (NIH/NIDDK) [F]
    Hi NMRPipe users. I have come across a problem, when I transform CBCACONH or HNCACB spectra using command Bruker and read the parameters, the data points of
    Message 1 of 2 , Sep 8, 2008
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      Hi NMRPipe users. I have come across a problem, when I transform CBCACONH or HNCACB spectra using command “Bruker” and read the parameters, the data points of C13 appear under z-axis column and that of N15 under the y-axis column. When I manually make changes in a way to put every parameter of C13 in y-axis and those of N-15 to z-axis and execute the script the resultant 2D xy-plan looks strange and xz-plan just weird. If I keep the parameters of C13 on z-axis and those of N15 on Y-axis the resultant 2d plans are perfect. But the problem is I want to keep C13 on Y to see the CH correlations while scrolling through N15 plans. These spectra were acquired using Topspin. I would highly appreciate if any one can help to fix the problem

       

      Syed

       

    • Nicholas Fitzkee
      Hi Syed, I m not an expert in NMRPipe by any means, but I think I can help you with this one. The bruker x, y, z columns are used to tell pipe the order in
      Message 2 of 2 , Sep 9, 2008
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        Hi Syed,
         
        I'm not an expert in NMRPipe by any means, but I think I can help you with this one.  The bruker x, y, z columns are used to tell pipe the order in which your FIDs were recorded (i.e., is CBCA chemical shift encoded during t1 or t2).  It's related to the XYZ order of the processed spectrum, but it's primarily dependent on your pulse program. Thus, as you discovered, you can't go changing the values arbitrarily and expect to get a sensible spectrum.
         
        What'd you'd like to do is transpose your processed spectrum so that nmrDraw displays the nitrogen planes along Z.  That is controlled during the final processing step, and you can transpose your processed spectrum using the following commands:
         
        xyz2pipe -in ft/test%03d.ft3 -z -verb \
        | nmrPipe  -fn ZTP \
        | pipe2xyz -out ft/ztp%03d.ft3 -z -ov
        You can also work the transpose in implicitly during the t1 processing step.  In the following set of pipes, I read in z planes (-z, in the first line) and write out those planes as y planes (-y, in the last line).  Since the original Z plane is my 13C dimension, the spectrum is transposed so that 13C is along Y.  This is my understanding, at least.  Please don't laugh at the phasing. :-)
         
        xyz2pipe -in ft/001A%03d.DAT -z -verb \
        | nmrPipe  -fn SP -off 0.38 -end 0.98 -pow 1 -c 1.0  \
        | nmrPipe  -fn ZF -size 128 \
        | nmrPipe  -fn FT \
        | nmrPipe  -fn PS -p0 -31.4 -p1 161.5 -di \
        | pipe2xyz -out ft/001B%03d.DAT -y -ov
        With this method, you may need to play around to get the correct result.
         
        Hope that helps,
        Nick

        --
        Nicholas Fitzkee, Ph.D.
        National Institutes of Health
        Laboratory of Chemical Physics, NIDDK

        e: nfitzkee@...
        w: (301) 451-7233
        f: (301) 496-0825

        -----Original Message-----
        From: nmrpipe@yahoogroups.com [mailto:nmrpipe@yahoogroups.com] On Behalf Of Hussan, Syed (NIH/NIDDK) [F]
        Sent: Monday, September 08, 2008 4:00 PM
        To: nmrpipe@yahoogroups.com
        Subject: [nmrpipe] CBCACONH conversion problem to NMRpipe formate

        Hi NMRPipe users. I have come across a problem, when I transform CBCACONH or HNCACB spectra using command “Bruker” and read the parameters, the data points of C13 appear under z-axis column and that of N15 under the y-axis column. When I manually make changes in a way to put every parameter of C13 in y-axis and those of N-15 to z-axis and execute the script the resultant 2D xy-plan looks strange and xz-plan just weird. If I keep the parameters of C13 on z-axis and those of N15 on Y-axis the resultant 2d plans are perfect. But the problem is I want to keep C13 on Y to see the CH correlations while scrolling through N15 plans. These spectra were acquired using Topspin. I would highly appreciate if any one can help to fix the problem

        Syed

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