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linear prediction in N15 dimension

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  • jhhong7546
    Hi all This time I wanna have your opinion about the linear prediction Recently I got the HNCO and HNCACB spectrum. Both of them looks good when they were
    Message 1 of 2 , Jul 9, 2007
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      Hi all

      This time I wanna have your opinion about the linear prediction

      Recently I got the HNCO and HNCACB spectrum. Both of them looks

      good when they were processed using just FT. but When I use

      Linear prediction in C13 and N15 dimension especially

      in N15 dimension spectrum became somewhat strange. for example

      some peak shape is severely distorted and can not be phased properly

      I adjusted points which is predicted and some other parameter

      but it could not become good. Is there any kind of something like

      rule for applying linear prediction about for example in certain

      case adding how much ponit is suitbale and above that spectrum

      will became very bad? This is my processing script

      for HNCO

      xyz2pipe -in fid/test_hnco%03d.fid -x -verb \
      | nmrPipe -fn POLY -time \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 159.0 -p1 0.0 \
      | nmrPipe -fn EXT -x1 6.5PPM -xn 10.5PPM -di -sw \
      | pipe2xyz -out lp/test_hnco%03d.ft3 -x -ov

      xyz2pipe -in lp/test_hnco%03d.ft3 -z -verb \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1.0 -c 0.67 \
      | nmrPipe -fn ZF -size 128 \
      | nmrPipe -fn FT -di \
      | pipe2xyz -out lp/fadddm_hnco%03d.ft3 -z -inPlace

      xyz2pipe -in lp/test_hnco%03d.ft3 -y -verb \
      | nmrPipe -fn LP -fb -pred 64 \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.33 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      #| nmrPipe -fn REV \
      | nmrPipe -fn PS -p0 7.0 -p1 0.0 -di \
      | nmrPipe -fn POLY -ord 1 \
      | pipe2xyz -out lp/test_hnco%03d.ft3 -y -inPlace

      xyz2pipe -in lp/test_hnco%03d.ft3 -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 -ps0-0 -pred 64 \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1.0 -c 0.67 \
      | nmrPipe -fn ZF -size 128 \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -hdr -di \
      | pipe2xyz -out lp/test_hnco%03d.DAT -z -inPlace

      HNCACB processing were done nearly same scheme
      Any kind of suggestion would be welcome about this problem

      Thanking in advance for kind and generous help!
    • Frank Delaglio Ph.D.
      oh my! there are numerous mistakes in the scheme. why are you scaling the first points of the FID with -c .33 or -c .66? this will introduce a baseline
      Message 2 of 2 , Jul 10, 2007
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        oh my!

        there are numerous mistakes in the scheme.

        why are you scaling the first points of the FID with
        -c .33 or -c .66? this will introduce a baseline distortion.

        scale the first point with -c 0.5 when there is no first order
        phase (i.e. no delay at the start of that dimension). leave the
        first point unchanged otherwise (-c 1.0)

        and, you are applying a baseline correction:

        POLY -ord 1

        but, you havent specified any baseline points. i,m not sure what
        will happen in this case, probably nothing. but, you shouldnt need
        any baseline correction here, especially if the first point scaling
        has been set correctly.

        now, most commonly, in a scheme where inverse processing is used,
        the inverse scheme may result in distortions of either the
        first or last point in the inverse-transform FID, or maybe even
        both. this will distort the LP results. this is especially true for
        mirror image LP. its safer to work with "LP -fb" at least until
        you figure out the other aspects of your scheme ... see the
        "LP" man page for more info.

        also, you have the wrong use of the "-inPlace" argument; this is
        only used when the source and destination names are the same.
        if you are "debugging" a processing scheme, its best not to
        use in-place mode at all, for one reason being that you
        can inspect the intermediate results.

        also also, you have a zero-fill value hard-wired into your scheme
        (ZF -size 128) ... this is a problem if your requested
        size is less than 2x the original time-domain size.

        if you want to fully explore the situation, first try LP
        in one dimension only:

        1. process the data as: X, then Y, then Z with "LP -fb"
        check that the result is ok.

        2. process the data as X, then Z, then Y with "LP -fb"
        check that the result is ok

        then, use your two-dimensional LP scheme, but save the
        interferogram as an intermediate step, for example:

        > xyz2pipe -in lp/test_hnco%03d.ft3 -z -verb \
        > | nmrPipe -fn HT -auto \
        > | nmrPipe -fn PS -inv -hdr \
        > | nmrPipe -fn FT -inv \
        > | nmrPipe -fn ZF -inv \
        > | nmrPipe -fn SP -inv -hdr \
        > | pipe2xyz -out lp/int%03d.dat

        then, have a look at the interferogram, to see if either the
        first points or last points are distorted. if the first
        point is distorted, this is probably a first-point scaling
        issue. if the last point is distorted, you can add an
        "EXT" to extract all but the last point (i.e. discard the
        bad last point) and then do LP.

        hope this helps ...





        --- In nmrpipe@yahoogroups.com, "jhhong7546" <croshong@...> wrote:
        >
        >
        > Hi all
        >
        > This time I wanna have your opinion about the linear prediction
        >
        > Recently I got the HNCO and HNCACB spectrum. Both of them looks
        >
        > good when they were processed using just FT. but When I use
        >
        > Linear prediction in C13 and N15 dimension especially
        >
        > in N15 dimension spectrum became somewhat strange. for example
        >
        > some peak shape is severely distorted and can not be phased
        properly
        >
        > I adjusted points which is predicted and some other parameter
        >
        > but it could not become good. Is there any kind of something like
        >
        > rule for applying linear prediction about for example in certain
        >
        > case adding how much ponit is suitbale and above that spectrum
        >
        > will became very bad? This is my processing script
        >
        > for HNCO
        >
        > xyz2pipe -in fid/test_hnco%03d.fid -x -verb \
        > | nmrPipe -fn POLY -time \
        > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 159.0 -p1 0.0 \
        > | nmrPipe -fn EXT -x1 6.5PPM -xn 10.5PPM -di -sw \
        > | pipe2xyz -out lp/test_hnco%03d.ft3 -x -ov
        >
        > xyz2pipe -in lp/test_hnco%03d.ft3 -z -verb \
        > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1.0 -c 0.67 \
        > | nmrPipe -fn ZF -size 128 \
        > | nmrPipe -fn FT -di \
        > | pipe2xyz -out lp/fadddm_hnco%03d.ft3 -z -inPlace
        >
        > xyz2pipe -in lp/test_hnco%03d.ft3 -y -verb \
        > | nmrPipe -fn LP -fb -pred 64 \
        > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.33 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > #| nmrPipe -fn REV \
        > | nmrPipe -fn PS -p0 7.0 -p1 0.0 -di \
        > | nmrPipe -fn POLY -ord 1 \
        > | pipe2xyz -out lp/test_hnco%03d.ft3 -y -inPlace
        >
        > xyz2pipe -in lp/test_hnco%03d.ft3 -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 -ps0-0 -pred 64 \
        > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1.0 -c 0.67 \
        > | nmrPipe -fn ZF -size 128 \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -hdr -di \
        > | pipe2xyz -out lp/test_hnco%03d.DAT -z -inPlace
        >
        > HNCACB processing were done nearly same scheme
        > Any kind of suggestion would be welcome about this problem
        >
        > Thanking in advance for kind and generous help!
        >
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