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nmrWish, I like it!

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  • ethernet3399
    Thanks, Dr. Delaglio! I know there is a lots of way to do the same thing. I have found nmrWish can do this job. I write the code like this: [chang@S102NMR2]#
    Message 1 of 4 , May 31, 2005
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      Thanks, Dr. Delaglio!
      I know there is a lots of way to do the same thing. I have found nmrWish can do
      this job. I write the code like this:

      [chang@S102NMR2]# nmrWish
      %readROI -in Processed/FT3/tmp%03d.ft3 -out hn.dat -x HN -y N15 -z CO
      %writeROI -out hn.dat
      %exit

      Then, in the current directory, a file with name "hn.dat" appeared. I can use
      nmrDraw to open it. It's a N15-HSQC like spectrum from HNCO. In fact, it's the
      projection.

      The nmrWish manual says it can extract strip too! I now can extract the strip, but
      have no idea to draw it. The drawROI no effect. Such as:

      [chang@S102NMR2]# nmrWish
      %readROI -in Processed/FT3/hnco%03d.ft3 -out strip1.dat -roi strip1 -ov -center X
      -dx HN 9.6ppm 0.12ppm -y C13 0% 100% -dz N15 121.6ppm 1
      %drawROI -roi strip1
      %writeROI -out strip1.dat
      %exit

      But no response in the nmrWish window, can you offer me a thorough explanation
      about nmrWish, and some example scripts. Thanks you! I am very interested in
      "nmrWish".

      Tieying Zhang
      2005,06,01

      --- In nmrpipe@yahoogroups.com, Frank Delaglio <delaglio@s...> wrote:
      >
      > Extracts the first XZ plane from a 3D hypercomplex FID:
      >
      > $NMRTXT/ext.xz.com fid/test%03d.fid xz001.fid
      >
      > Or, add one more argument to extract the Nth XZ plane:
      >
      > $NMRTXT/ext.xz.com fid/test%03d.fid xz002.fid 2
      >
      >
      > On Sat, 28 May 2005, ethernet3399 wrote:
      >
      > > Hi, all!
      > > Yesterday I try to extract a N15-Hsqc-like sub-spectrum from a hnco 3D
      > > fid matrix, but I have some difficulity while doing that. After discussion with
      > > collaborator and reading the nmrPipe manual carefully, I have solve the
      > > problem.
      > >
      > > The original axis order in hnco spectrum is HN, CO, N15. First I want to
      > > transpose the axis' order, so I write the script as:
      > >
      > > xyz2pipe -in $wdir/Processed/tmp-fid/tmp%03d.fid -z \
      > > |pipe2xyz -out $wdir/Processed/zxfid/tmp%03d.fid -x
      > >
      > > I omit a parameter "-ri2c" in xyz2pipe command. So the correct script may
      > > be:
      > >
      > > xyz2pipe -in $wdir/Processed/tmp-fid/tmp%03d.fid -z -ri2c \
      > > |nmrPipe -fn TP -hyper \
      > > |pipe2xyz -out $wdir/Processed/xzfid/tmp%03d.fid -x
      > >
      > > Now everything is OK. Then do FT transform for the xzfid matrix in the
      first
      > > two axis as usual, leave the third axis in time-domain.
      > >
      > > Who knows how to do this by nmrWish? I would appreciat any advice!
      > >
      > > Tieying Zhang
      > > 2005,05,28
      > >
      > >
      > >
      > >
      > >
      > >
      > >
      > >
      > >
      > > Yahoo! Groups Links
      > >
      > >
      > >
      > >
      > >
      > >
      > >
    • Frank Delaglio
      Thanks for your comments! You can also find scripts com/proj3D.tcl and com/proj2D.tcl which are general purpose automated scripts for creating projections
      Message 2 of 4 , Jun 1 8:37 AM
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        Thanks for your comments!

        You can also find scripts com/proj3D.tcl and com/proj2D.tcl which
        are general purpose "automated" scripts for creating projections
        from 3D and 2D data ...


        On Wed, 1 Jun 2005, ethernet3399 wrote:

        > Thanks, Dr. Delaglio!
        > I know there is a lots of way to do the same thing. I have found nmrWish can do
        > this job. I write the code like this:
        >
        > [chang@S102NMR2]# nmrWish
        > %readROI -in Processed/FT3/tmp%03d.ft3 -out hn.dat -x HN -y N15 -z CO
        > %writeROI -out hn.dat
        > %exit
        >
        > Then, in the current directory, a file with name "hn.dat" appeared. I can use
        > nmrDraw to open it. It's a N15-HSQC like spectrum from HNCO. In fact, it's the
        > projection.
        >
        > The nmrWish manual says it can extract strip too! I now can extract the strip, but
        > have no idea to draw it. The drawROI no effect. Such as:
        >
        > [chang@S102NMR2]# nmrWish
        > %readROI -in Processed/FT3/hnco%03d.ft3 -out strip1.dat -roi strip1 -ov -center X
        > -dx HN 9.6ppm 0.12ppm -y C13 0% 100% -dz N15 121.6ppm 1
        > %drawROI -roi strip1
        > %writeROI -out strip1.dat
        > %exit
        >
        > But no response in the nmrWish window, can you offer me a thorough explanation
        > about nmrWish, and some example scripts. Thanks you! I am very interested in
        > "nmrWish".
        >
        > Tieying Zhang
        > 2005,06,01
        >
        > --- In nmrpipe@yahoogroups.com, Frank Delaglio <delaglio@s...> wrote:
        > >
        > > Extracts the first XZ plane from a 3D hypercomplex FID:
        > >
        > > $NMRTXT/ext.xz.com fid/test%03d.fid xz001.fid
        > >
        > > Or, add one more argument to extract the Nth XZ plane:
        > >
        > > $NMRTXT/ext.xz.com fid/test%03d.fid xz002.fid 2
        > >
        > >
        > > On Sat, 28 May 2005, ethernet3399 wrote:
        > >
        > > > Hi, all!
        > > > Yesterday I try to extract a N15-Hsqc-like sub-spectrum from a hnco 3D
        > > > fid matrix, but I have some difficulity while doing that. After discussion with
        > > > collaborator and reading the nmrPipe manual carefully, I have solve the
        > > > problem.
        > > >
        > > > The original axis order in hnco spectrum is HN, CO, N15. First I want to
        > > > transpose the axis' order, so I write the script as:
        > > >
        > > > xyz2pipe -in $wdir/Processed/tmp-fid/tmp%03d.fid -z \
        > > > |pipe2xyz -out $wdir/Processed/zxfid/tmp%03d.fid -x
        > > >
        > > > I omit a parameter "-ri2c" in xyz2pipe command. So the correct script may
        > > > be:
        > > >
        > > > xyz2pipe -in $wdir/Processed/tmp-fid/tmp%03d.fid -z -ri2c \
        > > > |nmrPipe -fn TP -hyper \
        > > > |pipe2xyz -out $wdir/Processed/xzfid/tmp%03d.fid -x
        > > >
        > > > Now everything is OK. Then do FT transform for the xzfid matrix in the
        > first
        > > > two axis as usual, leave the third axis in time-domain.
        > > >
        > > > Who knows how to do this by nmrWish? I would appreciat any advice!
        > > >
        > > > Tieying Zhang
        > > > 2005,05,28
        > > >
        > > >
        > > >
        > > >
        > > >
        > > >
        > > >
        > > >
        > > >
        > > > Yahoo! Groups Links
        > > >
        > > >
        > > >
        > > >
        > > >
        > > >
        > > >
        >
        >
        >
        >
        >
        >
        >
        >
        >
        > Yahoo! Groups Links
        >
        >
        >
        >
        >
        >
        >
        >
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