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problems in linear prediction for both indirect diemnsions in CCH cosy experiment

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  • Weidong Hu
    Dear NMRPipe users, I am processing constant time version of CCH cosy experiment. I would like to apply the linear prediction for both carbon dimensions. I can
    Message 1 of 4 , Feb 15, 2011
      Dear NMRPipe users,

      I am processing constant time version of CCH cosy experiment. I would like to apply the linear prediction for both carbon dimensions. I can do the linear prediction for y axis. But if I do the HT and predict z axis, the data seems messed up, there are only a lot wiggles along the y axis. The attached is the micro I used. Everything works fine if I only commend out the line of second LP function. It suggests somehow, I could not apply the LP on the Z axis, I don't understand why that happens. Could some one give me some hints what is going on?

      Thank you in advance.


      Weidong Hu
      City of Hope
      Duarte, CA

      The following is the micro I used.

      # Addition for multiprocessors plus -par pipe.net in xyz2pipe line

      xyz2pipe -in fid/test%03d.fid -x -verb \
      # | nmrPipe -fn SOL \
      | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 15.6 -p1 -0.0 -di \
      | nmrPipe -fn POLY -auto -ord 0 \
      | nmrPipe -fn EXT -right -sw \
      | pipe2xyz -out lptest/tt%03d.DAT -x -ov

      xyz2pipe -in lptest/tt%03d.DAT -z -verb \
      | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT -auto \
      | nmrPipe -fn PS -p0 -0 -p1 0 -di \
      | nmrPipe -fn POLY -auto -ord 0 \
      # | nmrPipe -fn REV \
      | pipe2xyz -out lptest_1/tt%03d.DAT -z -ov

      xyz2pipe -in lptest_1/tt%03d.DAT -y -verb \
      | nmrPipe -fn LP -fb \
      | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT -alt \
      | nmrPipe -fn PS -p0 0.8 -p1 0 -di \
      | nmrPipe -fn POLY -auto -ord 0 \
      | nmrPipe -fn CS -ls 17ppm -sw \
      # | nmrPipe -fn REV \
      | pipe2xyz -out lptest_2/tt%03d.DAT -y -ov

      xyz2pipe -in lptest_2/tt%03d.DAT -z -verb \
      | nmrPipe -fn HT -auto \
      | nmrPipe -fn PS -inv -hdr \
      | nmrPipe -fn FT -inv \
      | nmrPipe -fn ZF -inv \
      | nmrPipe -fn SP -inv -hdr \
      | nmrPipe -fn LP -fb \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
      | nmrPipe -fn ZF -size 128 \
      | nmrPipe -fn FT -auto \
      | nmrPipe -fn PS -p0 0 -p1 0 -di \
      | nmrPipe -fn POLY -auto -ord 0 \
      | nmrPipe -fn CS -ls 5ppm -sw \
      | pipe2xyz -out lptest_3/tt%03d.DAT -z -ov
    • Frank Delaglio
      Ok, just as a check, be sure that an ordinary FT of your data looks good if you havent done this already. Inverse processing divides by the previously-applied
      Message 2 of 4 , Feb 16, 2011
        Ok, just as a check, be sure that an ordinary FT of your data
        looks good if you havent done this already.

        Inverse processing divides by the previously-applied window.
        So, try a more conservative window function, one that doesn't
        go too close to zero at the end, such as:

        nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 ...

        If this doesn't help, save the interferogram just before the
        last LP step, and have a look. The data in the inverse-processed
        dimension should look like undistorted sinusoids.

        Also, your first-point scaling values -c are wrong in every
        dimension, which will cause baseline offsets. The first
        point scaling should be -c 0.5 whenever the corresponding
        first-order phase is around zero. If you do this, you can
        probably remove all the baseline correction steps.

        Can't say if your last ZF "-size 128" is acceptable, since we
        don't know the original size of the data. Usually
        it is better to have "ZF -auto", which will always be suitable.

        Finally, your script shows prior use of "REV" ... although it
        is commented out, keep in mind that use of REV is usually wrong.
        If a dimension is reversed, use "FT -neg" to process it,
        otherwise your chemical shift calibration will be wrong by
        one point.





        Quoting Weidong Hu <lakesu@...>:

        > Dear NMRPipe users,
        >
        > I am processing constant time version of CCH cosy experiment. I
        > would like to apply the linear prediction for both carbon
        > dimensions. I can do the linear prediction for y axis. But if I do
        > the HT and predict z axis, the data seems messed up, there are only
        > a lot wiggles along the y axis. The attached is the micro I used.
        > Everything works fine if I only commend out the line of second LP
        > function. It suggests somehow, I could not apply the LP on the Z
        > axis, I don't understand why that happens. Could some one give me
        > some hints what is going on?
        >
        > Thank you in advance.
        >
        >
        > Weidong Hu
        > City of Hope
        > Duarte, CA
        >
        > The following is the micro I used.
        >
        > # Addition for multiprocessors plus -par pipe.net in xyz2pipe line
        >
        > xyz2pipe -in fid/test%03d.fid -x -verb \
        > # | nmrPipe -fn SOL \
        > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 15.6 -p1 -0.0 -di \
        > | nmrPipe -fn POLY -auto -ord 0 \
        > | nmrPipe -fn EXT -right -sw \
        > | pipe2xyz -out lptest/tt%03d.DAT -x -ov
        >
        > xyz2pipe -in lptest/tt%03d.DAT -z -verb \
        > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT -auto \
        > | nmrPipe -fn PS -p0 -0 -p1 0 -di \
        > | nmrPipe -fn POLY -auto -ord 0 \
        > # | nmrPipe -fn REV \
        > | pipe2xyz -out lptest_1/tt%03d.DAT -z -ov
        >
        > xyz2pipe -in lptest_1/tt%03d.DAT -y -verb \
        > | nmrPipe -fn LP -fb \
        > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT -alt \
        > | nmrPipe -fn PS -p0 0.8 -p1 0 -di \
        > | nmrPipe -fn POLY -auto -ord 0 \
        > | nmrPipe -fn CS -ls 17ppm -sw \
        > # | nmrPipe -fn REV \
        > | pipe2xyz -out lptest_2/tt%03d.DAT -y -ov
        >
        > xyz2pipe -in lptest_2/tt%03d.DAT -z -verb \
        > | nmrPipe -fn HT -auto \
        > | nmrPipe -fn PS -inv -hdr \
        > | nmrPipe -fn FT -inv \
        > | nmrPipe -fn ZF -inv \
        > | nmrPipe -fn SP -inv -hdr \
        > | nmrPipe -fn LP -fb \
        > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
        > | nmrPipe -fn ZF -size 128 \
        > | nmrPipe -fn FT -auto \
        > | nmrPipe -fn PS -p0 0 -p1 0 -di \
        > | nmrPipe -fn POLY -auto -ord 0 \
        > | nmrPipe -fn CS -ls 5ppm -sw \
        > | pipe2xyz -out lptest_3/tt%03d.DAT -z -ov
        >
        >
        >
      • Weidong Hu
        Dear Frank,   Thank you very much for going through the script and pointing out several places need to be corrected or checked out. I will follow what you
        Message 3 of 4 , Feb 16, 2011
          Dear Frank,
           
          Thank you very much for going through the script and pointing out several places need to be corrected or checked out. I will follow what you suggested and check them out.
           
          Before I sent out email for help. I did some trouble shooting. The normal FT gives good spectrum, the normal FT with LP in y axis gives good spectrum. I also applied all the inverse FT related functions in y axis with just LP command left out, it still gives good data. Only when I added the LP in the Y axis, all the wiggles showed up, and the cross peaks are messed up. 
           
          I will go through the suggestions you gave and see what I get.
           
          Best regards,
           
          Weidong

          --- On Wed, 2/16/11, Frank Delaglio <delaglio@...> wrote:

          From: Frank Delaglio <delaglio@...>
          Subject: Re: [nmrpipe] problems in linear prediction for both indirect diemnsions in CCH cosy experiment
          To: nmrpipe@yahoogroups.com
          Date: Wednesday, February 16, 2011, 10:10 AM

           

          Ok, just as a check, be sure that an ordinary FT of your data
          looks good if you havent done this already.

          Inverse processing divides by the previously-applied window.
          So, try a more conservative window function, one that doesn't
          go too close to zero at the end, such as:

          nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 ...

          If this doesn't help, save the interferogram just before the
          last LP step, and have a look. The data in the inverse-processed
          dimension should look like undistorted sinusoids.

          Also, your first-point scaling values -c are wrong in every
          dimension, which will cause baseline offsets. The first
          point scaling should be -c 0.5 whenever the corresponding
          first-order phase is around zero. If you do this, you can
          probably remove all the baseline correction steps.

          Can't say if your last ZF "-size 128" is acceptable, since we
          don't know the original size of the data. Usually
          it is better to have "ZF -auto", which will always be suitable.

          Finally, your script shows prior use of "REV" ... although it
          is commented out, keep in mind that use of REV is usually wrong.
          If a dimension is reversed, use "FT -neg" to process it,
          otherwise your chemical shift calibration will be wrong by
          one point.

          Quoting Weidong Hu <lakesu@...>:

          > Dear NMRPipe users,
          >
          > I am processing constant time version of CCH cosy experiment. I
          > would like to apply the linear prediction for both carbon
          > dimensions. I can do the linear prediction for y axis. But if I do
          > the HT and predict z axis, the data seems messed up, there are only
          > a lot wiggles along the y axis. The attached is the micro I used.
          > Everything works fine if I only commend out the line of second LP
          > function. It suggests somehow, I could not apply the LP on the Z
          > axis, I don't understand why that happens. Could some one give me
          > some hints what is going on?
          >
          > Thank you in advance.
          >
          >
          > Weidong Hu
          > City of Hope
          > Duarte, CA
          >
          > The following is the micro I used.
          >
          > # Addition for multiprocessors plus -par pipe.net in xyz2pipe line
          >
          > xyz2pipe -in fid/test%03d.fid -x -verb \
          > # | nmrPipe -fn SOL \
          > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1 \
          > | nmrPipe -fn ZF -auto \
          > | nmrPipe -fn FT \
          > | nmrPipe -fn PS -p0 15.6 -p1 -0.0 -di \
          > | nmrPipe -fn POLY -auto -ord 0 \
          > | nmrPipe -fn EXT -right -sw \
          > | pipe2xyz -out lptest/tt%03d.DAT -x -ov
          >
          > xyz2pipe -in lptest/tt%03d.DAT -z -verb \
          > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
          > | nmrPipe -fn ZF -auto \
          > | nmrPipe -fn FT -auto \
          > | nmrPipe -fn PS -p0 -0 -p1 0 -di \
          > | nmrPipe -fn POLY -auto -ord 0 \
          > # | nmrPipe -fn REV \
          > | pipe2xyz -out lptest_1/tt%03d.DAT -z -ov
          >
          > xyz2pipe -in lptest_1/tt%03d.DAT -y -verb \
          > | nmrPipe -fn LP -fb \
          > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
          > | nmrPipe -fn ZF -auto \
          > | nmrPipe -fn FT -alt \
          > | nmrPipe -fn PS -p0 0.8 -p1 0 -di \
          > | nmrPipe -fn POLY -auto -ord 0 \
          > | nmrPipe -fn CS -ls 17ppm -sw \
          > # | nmrPipe -fn REV \
          > | pipe2xyz -out lptest_2/tt%03d.DAT -y -ov
          >
          > xyz2pipe -in lptest_2/tt%03d.DAT -z -verb \
          > | nmrPipe -fn HT -auto \
          > | nmrPipe -fn PS -inv -hdr \
          > | nmrPipe -fn FT -inv \
          > | nmrPipe -fn ZF -inv \
          > | nmrPipe -fn SP -inv -hdr \
          > | nmrPipe -fn LP -fb \
          > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
          > | nmrPipe -fn ZF -size 128 \
          > | nmrPipe -fn FT -auto \
          > | nmrPipe -fn PS -p0 0 -p1 0 -di \
          > | nmrPipe -fn POLY -auto -ord 0 \
          > | nmrPipe -fn CS -ls 5ppm -sw \
          > | pipe2xyz -out lptest_3/tt%03d.DAT -z -ov
          >
          >
          >

        • Weidong Hu
          Dear Frank,   Thank you very much for your help.   It worked now. The main change as you suggested is from     ... to   ...   for both indirect
          Message 4 of 4 , Feb 16, 2011
            Dear Frank,
             
            Thank you very much for your help.
             
            It worked now. The main change as you suggested is from  
             
            | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
            to
             
            | nmrPipe -fn SP -off 0.5 -end 0.95 -pow 2 -c 0.5\
             
            for both indirect dimensions. The following is the script worked.
             
            Thank you again for your great help!
             
             

            # Addition for multiprocessors plus -par pipe.net in xyz2pipe line

            xyz2pipe -in fid/test%03d.fid -x -verb    \
            # | nmrPipe  -fn SOL                                          \
            | nmrPipe  -fn SP -off 0.48 -end 0.99 -pow 2 -c 1             \
            | nmrPipe  -fn ZF -auto                                          \
            | nmrPipe  -fn FT                                                \
            | nmrPipe  -fn PS -p0 17.2  -p1 -0.0 -di                               \
            | nmrPipe  -fn POLY -auto -ord 0                                 \
            | nmrPipe  -fn EXT -right -sw                         \
            | pipe2xyz -out lptest/tt%03d.DAT -x -ov

            xyz2pipe -in lptest/tt%03d.DAT -z -verb                            \
            | nmrPipe  -fn SP -off 0.5 -end 0.95 -pow 2 -c 0.5              \
            | nmrPipe  -fn ZF -auto                                    \
            | nmrPipe  -fn FT -auto                                               \
            | nmrPipe  -fn PS -p0 -0  -p1 0  -di                              \
            # | nmrPipe  -fn POLY -auto -ord 0                                  \
            # | nmrPipe  -fn REV              \
            | pipe2xyz -out lptest_1/tt%03d.DAT -z -ov

            xyz2pipe -in lptest_1/tt%03d.DAT -y -verb    \
            | nmrPipe  -fn LP -fb                                          \
            | nmrPipe  -fn SP -off 0.5 -end 0.95 -pow 2 -c 0.5              \
            | nmrPipe  -fn ZF -auto                                          \
            | nmrPipe  -fn FT -alt                                                  \
            | nmrPipe  -fn PS -p0 0.8 -p1 0 -di                           \
            # | nmrPipe  -fn POLY -auto -ord 0                                  \
            | nmrPipe  -fn CS -ls 17ppm -sw                                      \
            # | nmrPipe  -fn REV              \
            | pipe2xyz -out lptest_2/tt%03d.DAT -y -ov

            xyz2pipe -in lptest_2/tt%03d.DAT -z -verb                            \
            | nmrPipe  -fn HT -auto                                         \
            | nmrPipe  -fn PS -inv -hdr                                          \
            | nmrPipe  -fn FT -inv                                           \
            | nmrPipe  -fn ZF -inv                                           \
            | nmrPipe  -fn SP -inv -hdr          \
            | nmrPipe  -fn LP -fb                  \
            | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5              \
            | nmrPipe  -fn ZF -auto                                    \
            | nmrPipe  -fn FT -auto                                                 \
            | nmrPipe  -fn PS -p0 0 -p1 0 -di                              \
            # | nmrPipe  -fn POLY -auto -ord 0                                  \
            | nmrPipe  -fn CS -ls 5ppm -sw                                      \
            | pipe2xyz -out  lptest_3/tt%03d.DAT -z -ov
             


            --- On Wed, 2/16/11, Frank Delaglio <delaglio@...> wrote:

            From: Frank Delaglio <delaglio@...>
            Subject: Re: [nmrpipe] problems in linear prediction for both indirect diemnsions in CCH cosy experiment
            To: nmrpipe@yahoogroups.com
            Date: Wednesday, February 16, 2011, 10:10 AM

             

            Ok, just as a check, be sure that an ordinary FT of your data
            looks good if you havent done this already.

            Inverse processing divides by the previously-applied window.
            So, try a more conservative window function, one that doesn't
            go too close to zero at the end, such as:

            nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 ...

            If this doesn't help, save the interferogram just before the
            last LP step, and have a look. The data in the inverse-processed
            dimension should look like undistorted sinusoids.

            Also, your first-point scaling values -c are wrong in every
            dimension, which will cause baseline offsets. The first
            point scaling should be -c 0.5 whenever the corresponding
            first-order phase is around zero. If you do this, you can
            probably remove all the baseline correction steps.

            Can't say if your last ZF "-size 128" is acceptable, since we
            don't know the original size of the data. Usually
            it is better to have "ZF -auto", which will always be suitable.

            Finally, your script shows prior use of "REV" ... although it
            is commented out, keep in mind that use of REV is usually wrong.
            If a dimension is reversed, use "FT -neg" to process it,
            otherwise your chemical shift calibration will be wrong by
            one point.

            Quoting Weidong Hu <lakesu@...>:

            > Dear NMRPipe users,
            >
            > I am processing constant time version of CCH cosy experiment. I
            > would like to apply the linear prediction for both carbon
            > dimensions. I can do the linear prediction for y axis. But if I do
            > the HT and predict z axis, the data seems messed up, there are only
            > a lot wiggles along the y axis. The attached is the micro I used.
            > Everything works fine if I only commend out the line of second LP
            > function. It suggests somehow, I could not apply the LP on the Z
            > axis, I don't understand why that happens. Could some one give me
            > some hints what is going on?
            >
            > Thank you in advance.
            >
            >
            > Weidong Hu
            > City of Hope
            > Duarte, CA
            >
            > The following is the micro I used.
            >
            > # Addition for multiprocessors plus -par pipe.net in xyz2pipe line
            >
            > xyz2pipe -in fid/test%03d.fid -x -verb \
            > # | nmrPipe -fn SOL \
            > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1 \
            > | nmrPipe -fn ZF -auto \
            > | nmrPipe -fn FT \
            > | nmrPipe -fn PS -p0 15.6 -p1 -0.0 -di \
            > | nmrPipe -fn POLY -auto -ord 0 \
            > | nmrPipe -fn EXT -right -sw \
            > | pipe2xyz -out lptest/tt%03d.DAT -x -ov
            >
            > xyz2pipe -in lptest/tt%03d.DAT -z -verb \
            > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
            > | nmrPipe -fn ZF -auto \
            > | nmrPipe -fn FT -auto \
            > | nmrPipe -fn PS -p0 -0 -p1 0 -di \
            > | nmrPipe -fn POLY -auto -ord 0 \
            > # | nmrPipe -fn REV \
            > | pipe2xyz -out lptest_1/tt%03d.DAT -z -ov
            >
            > xyz2pipe -in lptest_1/tt%03d.DAT -y -verb \
            > | nmrPipe -fn LP -fb \
            > | nmrPipe -fn SP -off 0.48 -end 0.99 -pow 2 -c 1.0 \
            > | nmrPipe -fn ZF -auto \
            > | nmrPipe -fn FT -alt \
            > | nmrPipe -fn PS -p0 0.8 -p1 0 -di \
            > | nmrPipe -fn POLY -auto -ord 0 \
            > | nmrPipe -fn CS -ls 17ppm -sw \
            > # | nmrPipe -fn REV \
            > | pipe2xyz -out lptest_2/tt%03d.DAT -y -ov
            >
            > xyz2pipe -in lptest_2/tt%03d.DAT -z -verb \
            > | nmrPipe -fn HT -auto \
            > | nmrPipe -fn PS -inv -hdr \
            > | nmrPipe -fn FT -inv \
            > | nmrPipe -fn ZF -inv \
            > | nmrPipe -fn SP -inv -hdr \
            > | nmrPipe -fn LP -fb \
            > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
            > | nmrPipe -fn ZF -size 128 \
            > | nmrPipe -fn FT -auto \
            > | nmrPipe -fn PS -p0 0 -p1 0 -di \
            > | nmrPipe -fn POLY -auto -ord 0 \
            > | nmrPipe -fn CS -ls 5ppm -sw \
            > | pipe2xyz -out lptest_3/tt%03d.DAT -z -ov
            >
            >
            >

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