Loading ...
Sorry, an error occurred while loading the content.

Re: [nmrpipe] 1D spectrum substraction

Expand Messages
  • Lei Li
    Thank you very much! ... ____________________________________________________________________________________ Need a quick answer? Get one in minutes from
    Message 1 of 8 , Jan 31, 2007
    • 0 Attachment
      Thank you very much!

      --- James <james.swarbrick@...> wrote:

      > Lei Li wrote:
      > >
      > > Dear All
      > >
      > > I have two 1D spectrum and I want to substract one
      > > from another. Can I do this in nmrPipe? Should it
      > be
      > > done in frequency domain (spectra) or time domain
      > > (fid)?How?
      > >
      > > Thank you very much!
      > >
      > > Lei
      > >
      > >
      >
      __________________________________________________________
      > > TV dinner still cooling?
      > > Check out "Tonight's Picks" on Yahoo! TV.
      > > http://tv.yahoo.com/ <http://tv.yahoo.com/>
      > >
      > >
      >
      > Hi
      > You can use the addNMR command either way. but as F
      > pointed out (check
      > archives) the phasing may be different between the
      > two).
      > For example you can add all your fids and have a
      > pesudo 2D but when you
      > scan through them in nmrDraw you probably wont be
      > able to phase them
      > simultaneously.
      >
      > So stick with the frequency:
      > addNMR -in1 spectrum1.dat -in2 spectrum2.dat -out
      > sub.dat -sub
      > see addNMR -help
      > james
      >




      ____________________________________________________________________________________
      Need a quick answer? Get one in minutes from people who know.
      Ask your question on www.Answers.yahoo.com
    • christiane riedinger
      dear pipers, i am having the same problem as mike osborne in 2005: -- HI Frank I have been trying to look through the dosyView.tcl script to help analyse my
      Message 2 of 8 , Feb 2, 2007
      • 0 Attachment
        dear pipers,

        i am having the same problem as mike osborne in 2005:

        --
        HI Frank
        I have been trying to look through the dosyView.tcl script to help
        analyse my translational diffusion data. However, I am not so clear as
        to how it works. Obviously there are inputs for gradient strength and
        Delays that I need to input. Is there an option for this or should I
        rewrite some of the code for my purposes..
        Thanks in advance for any help
        Cheers
        Mike
        --

        has anyone found a solution to this problem?

        best wishes,
        christiane.
      • ozzy672003
        Hi Christiane You can ask it to run a file containing the gradient strength (well, G^2delta^2 etc) directly include them.. ... #!/bin/csh ... #| nmrPipe -fn
        Message 3 of 8 , Feb 2, 2007
        • 0 Attachment
          Hi Christiane


          You can ask it to run a file containing the gradient strength (well,
          G^2delta^2 etc) directly include them..
          I have attached below an exanple script which specifies the tau values:
          ------------------------------------------
          #!/bin/csh

          | nmrPipe -fn POLY -time \
          | nmrPipe -fn EM -lb 6 -c 0.5 \
          #| nmrPipe -fn SP -off 0.25 -end 0.98 -pow 2 -c 0.5 \
          | nmrPipe -fn ZF -size 64000 \
          | nmrPipe -fn FT -verb \
          | nmrPipe -fn PS -p0 98 -p1 0 -di \
          | nmrPipe -fn EXT -x1 11ppm -xn 6.5ppm -sw \

          | nmrPipe -out test.ft1 -ov -verb


          dosyView.tcl -tau 7561.15 1701260 47257.2 1277830 120978 999962 228725
          756115 370496 546293 -zoom 1000
          ---------------------------------------------

          OR YOU CAN SPECIFY THE TAU VALUES IN A FILE replace the dosyView.tcl
          ilne with
          dosyView.tcl -tau -`cat ./taulist` -zoom 4000
          where taulist is the filename with


          Hope this helps.
          Cheers
          Mike


          -- In nmrpipe@yahoogroups.com, christiane riedinger
          <christiane.riedinger@...> wrote:
          >
          > dear pipers,
          >
          > i am having the same problem as mike osborne in 2005:
          >
          > --
          > HI Frank
          > I have been trying to look through the dosyView.tcl script to help
          > analyse my translational diffusion data. However, I am not so clear as
          > to how it works. Obviously there are inputs for gradient strength and
          > Delays that I need to input. Is there an option for this or should I
          > rewrite some of the code for my purposes..
          > Thanks in advance for any help
          > Cheers
          > Mike
          > --
          >
          > has anyone found a solution to this problem?
          >
          > best wishes,
          > christiane.
          >
        • Frank Delaglio, Ph.D. (CONTRACTOR)
          Ahoy!! Have a look at: dosyView.tcl -help fitXY.tcl -help The dosyFit.tcl script is a crude little application to fit selected lines from a 2D DOSY to a
          Message 4 of 8 , Feb 2, 2007
          • 0 Attachment
            Ahoy!!

            Have a look at:

            dosyView.tcl -help
            fitXY.tcl -help

            The "dosyFit.tcl" script is a crude little application to
            fit selected lines from a 2D DOSY to a single evolution.
            If you have overlapped lines, or multi-term diffusion to
            consider, than a different approach is needed.

            The "fitXY.tcl" is a general purpose module for fitting
            X,Y pairs of points to common functions such as exponentials
            and gaussians.

            The delays for "dosyView.tcl" are specified via the "-tau ..." argument.

            When a line is selected for fitting from the "dosyView" graphical
            interface, the corresponding list of intensities for that line's DOSY
            evolution is sent to the fitting script "fitXY.tcl". The intensities
            are the "y" coords for the fit, and the specified "-tau" values form
            the "x" coords. The command for performing the fit is saved in a
            script "dosyFit.com", which is executed in the background.

            Depending on how you arrange things, the DOSY data can
            be fit to either a gaussian or an exponential. In either case,
            a general decay factor will be reported, and you will have to
            transform this appropriately to convert it to a diffusion
            value:

            y = amp*exp( alpha*x ) (exponential)
            y = amp*exp( alpha*x*x ) (gaussian "dosyView.tcl .... -aux -gauss")

            where "amp" is an intensity scaling factor,
            and "alpha" is a decay value.



            On Fri, 2 Feb 2007, christiane riedinger wrote:

            > dear pipers,
            >
            > i am having the same problem as mike osborne in 2005:
            >
            > --
            > HI Frank
            > I have been trying to look through the dosyView.tcl script to help
            > analyse my translational diffusion data. However, I am not so clear as
            > to how it works. Obviously there are inputs for gradient strength and
            > Delays that I need to input. Is there an option for this or should I
            > rewrite some of the code for my purposes..
            > Thanks in advance for any help
            > Cheers
            > Mike
            > --
            >
            > has anyone found a solution to this problem?
            >
            > best wishes,
            > christiane.
            >
            >
            >
            >
            >
          • Frank Delaglio, Ph.D. (CONTRACTOR)
            HUZZAH!! 3 cheers for Mike O ... one little change is needed perhaps ... ... this should probably be (note the removal of one - ): dosyView.tcl -tau `cat
            Message 5 of 8 , Feb 2, 2007
            • 0 Attachment
              HUZZAH!! 3 cheers for Mike O ...
              one little change is needed perhaps ...

              > dosyView.tcl -tau -`cat ./taulist` -zoom 4000
              > where taulist is the filename

              this should probably be (note the removal of one "-"):

              dosyView.tcl -tau `cat ./taulist` -zoom 4000

              On Fri, 2 Feb 2007, ozzy672003 wrote:

              > Hi Christiane
              >
              >
              > You can ask it to run a file containing the gradient strength (well,
              > G^2delta^2 etc) directly include them..=20
              > I have attached below an exanple script which specifies the tau values:
              > ------------------------------------------
              > #!/bin/csh
              >
              > | nmrPipe -fn POLY -time \
              > | nmrPipe -fn EM -lb 6 -c 0.5 \
              > #| nmrPipe -fn SP -off 0.25 -end 0.98 -pow 2 -c 0.5 \
              > | nmrPipe -fn ZF -size 64000 \
              > | nmrPipe -fn FT -verb \
              > | nmrPipe -fn PS -p0 98 -p1 0 -di \
              > | nmrPipe -fn EXT -x1 11ppm -xn 6.5ppm -sw \=20=20
              > =20=20=20=20=20=20=20=20
              > | nmrPipe -out test.ft1 -ov -verb
              >
              >
              > dosyView.tcl -tau 7561.15 1701260 47257.2 1277830 120978 999962 228725
              > 756115 370496 546293 -zoom 1000
              > ---------------------------------------------
              >
              > OR YOU CAN SPECIFY THE TAU VALUES IN A FILE replace the dosyView.tcl
              > ilne with=20
              > dosyView.tcl -tau -`cat ./taulist` -zoom 4000
              > where taulist is the filename with
              >
              >
              > Hope this helps.
              > Cheers
              > Mike
              >
              >
              > -- In nmrpipe@yahoogroups.com, christiane riedinger
              > <christiane.riedinger@...> wrote:
              > >
              > > dear pipers,
              > >=20
              > > i am having the same problem as mike osborne in 2005:
              > >=20
              > > --
              > > HI Frank
              > > I have been trying to look through the dosyView.tcl script to help
              > > analyse my translational diffusion data. However, I am not so clear as
              > > to how it works. Obviously there are inputs for gradient strength and
              > > Delays that I need to input. Is there an option for this or should I
              > > rewrite some of the code for my purposes..
              > > Thanks in advance for any help
              > > Cheers
              > > Mike
              > > --
              > >=20
              > > has anyone found a solution to this problem?
              > >=20
              > > best wishes,
              > > christiane.
              > >
              >
              >
              >
            Your message has been successfully submitted and would be delivered to recipients shortly.