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Re: linear prediction in N15 dimension

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  • 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 1 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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