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  • yxz8@xx.xxxx.xxxxxxxxxxxxxxxxx)
    Hello, I am processing a couple of bruker datasets(HCCH-TOCSY, C13-NOESY and N15-NOESY, from AVANCE 800MHz) using nmrPipe. This is the first time I work with
    Message 1 of 7 , Jul 28, 1999
      Hello,

      I am processing a couple of bruker datasets(HCCH-TOCSY, C13-NOESY and
      N15-NOESY, from AVANCE 800MHz) using nmrPipe. This is the first time I
      work with bruker. If any relative scrips and hints can be given, that
      will really helpful to me.

      Thanks in advance.

      --
      Yongbo Zhang
      ************************************************************************
      *Department of Chemistry ** Telephone: 216/368-4476 (work)*
      *10900 Euclid Avenue ** Telephone: 216/231-6090 (home)*
      *Case Western Reserve University ** Fax: 216/368-3006 *
      *Cleveland, OH 44106-7078 ** E-mail: yxz8@... *
      ************************************************************************
    • Patti Liwang
      Hello Dr. Zhang, For bruk2pipe and nmrPipe documentation, go to http://www.resdesigns.com/ There are lots of examples there. Your letter implies you have
      Message 2 of 7 , Jul 28, 1999
        Hello Dr. Zhang,
        For bruk2pipe and nmrPipe documentation, go to
        http://www.resdesigns.com/

        There are lots of examples there.


        Your letter implies you have worked in the past with spectrometers other
        than Bruker. If this is the case, then your nmrPipe scripts (for
        processing) should all be the same. But the conversion programs (using say
        var2pipe) need to be altered a bit (to use bruk2pipe).

        Good luck!
        Patti LiWang




        >From: yxz8@... (Yongbo Zhang)
        >
        >
        >Hello,
        >
        >I am processing a couple of bruker datasets(HCCH-TOCSY, C13-NOESY and
        >N15-NOESY, from AVANCE 800MHz) using nmrPipe. This is the first time I
        >work with bruker. If any relative scrips and hints can be given, that
        >will really helpful to me.
        >
        >Thanks in advance.
        >
        >--
        >Yongbo Zhang
        >************************************************************************
        >*Department of Chemistry ** Telephone: 216/368-4476 (work)*
        >*10900 Euclid Avenue ** Telephone: 216/231-6090 (home)*
        >*Case Western Reserve University ** Fax: 216/368-3006 *
        >*Cleveland, OH 44106-7078 ** E-mail: yxz8@... *
        >************************************************************************
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        -------------------------------------------------------------
        Patricia LiWang
        Assistant Professor
        Department of Biochemistry and Biophysics
        Texas A&M University
        College Station, TX 77843-2128
        pliwang@...
        Phone: (409) 845-5616
        Fax: (409) 845-9274
      • Marta Maieron
        Hallo, I ve just started to use the NMRpipe program to process Bruker data. I would like to know if it is possible to phase 2D spectra in both dimentions.
        Message 3 of 7 , Aug 2, 1999
          Hallo,
          I've just started to use the NMRpipe program to process Bruker data.
          I would like to know if it is possible to phase 2D spectra in both
          dimentions.
          Until now I procedded the data whit macro took from tutorial.
          I have some problems to phase the 2D spectra in F1 dimention.
          Could anybody help me?

          Thanks in advance

          marta
          --
          ----
          Dr. Marta Maieron
          Dip. Scienze e Tecnologie Biomediche
          Universit´┐Ż di Udine
          Piazzale Kolbe, 4
          33100 Udine
          Italy
          Phone: +39-0432-494325
        • Istvan Pelczer
          Dear Marta, There are various ways to do this, one is to interrupt processing after t2-- F2 and transpose, then find phase parameters interactively. An
          Message 4 of 7 , Aug 2, 1999
            Dear Marta,
            There are various ways to do this, one is to interrupt processing after
            t2-->F2 and transpose, then find phase parameters interactively. An
            alternative is to take the final spectrum, extract F1 1D vectors, use
            Hilbert Transform to recreate the imaginary component, and find the
            optimal phase parameters. Then either you can do the same for the full
            spectrum or modify the original macro accordingly.
            If yo need more details please feel free to contact me.
            All the best,
            Istvan

            wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
            Istvan Pelczer, Ph.D. Email: ipelczer@...
            Senior NMR Spectroscopist
            Princeton University
            Department of Chemistry, Frick Lab., ph# (609) 258 2342
            Washington Road fax# (609) 258 6746
            Princeton, NJ 08544, USA

            Book Review Editor for "The NMR Newsletter"
            http://www.nmrnewsletter.com


            On Mon, 2 Aug 1999, Marta Maieron wrote:

            > From: Marta Maieron <MMaieron@...>
            >
            >
            > Hallo,
            > I've just started to use the NMRpipe program to process Bruker data.
            > I would like to know if it is possible to phase 2D spectra in both
            > dimentions.
            > Until now I procedded the data whit macro took from tutorial.
            > I have some problems to phase the 2D spectra in F1 dimention.
            > Could anybody help me?
            >
            > Thanks in advance
            >
            > marta
            > --
            > ----
            > Dr. Marta Maieron
            > Dip. Scienze e Tecnologie Biomediche
            > Universit´┐Ż di Udine
            > Piazzale Kolbe, 4
            > 33100 Udine
            > Italy
            > Phone: +39-0432-494325
            >
            >
            >
            >
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          • Frank Delaglio
            ... Interactive Phasing NMRDraw will automatically reconstruct imaginary data as needed, so it is always possible to interactively rephase any 1D spectral
            Message 5 of 7 , Aug 5, 1999
              Some notes and tips on phasing:

              ---
              Interactive Phasing

              NMRDraw will automatically reconstruct imaginary data as needed,
              so it is always possible to interactively rephase any 1D spectral
              vector being viewed, from any dimension:

              1. Use "1D/1D Vertical", "1D/Z-Axis" etc to activate 1D viewing mode.

              2. Use the mouse to select a 1D vector of interest.

              3. Click the "Phase" button in the command "On" to activate
              interactive phasing.

              4. Use the "P0" and "P1" sliders or text entries to adjust the phase as
              needed.

              Note that in any 1D viewing mode, when the mouse pointer is outside
              the 1D viewing area in the bottom or right border, dragging with
              the rightmost mouse button will change the position of the phase pivot
              point. The position of the pivot will be indicated on the 1D display
              by arrows. The pivot shows the position in the spectrum whose phase
              will stay fixed as P1 is adjusted.

              It is also possible to phase correct two or more vectors
              simultaneously. To keep a given vector on the screen,
              use the "1D/Append 1D" command. Then, continue to select
              other vectors to view with the mouse as usual. Any phase
              adjustments selected as above will be applied to all 1D
              vectors at once.

              ---
              Big FD's phase correction hints:

              0. When possible, take great care to acquire the data so that the
              indirect phases are known in advance.

              1. Always use trial processing of the first XY and XZ planes
              of a 3D to confirm overall phase corrections etc.

              2. Try at first to process the direct dimension without any
              first order phase.

              3. If you are not sure of the phase in an indirect dimension,
              try the "standard" values -90,180 and -180,360 before
              resorting to interactive phasing. If these don't work,
              try keeping the P1 at 180 or 360, and then adjusting only
              P0 interactively.

              4. If the "standard" values don't work, move the pivot to
              the exact center of the spectrum, set P0 to 0.0, and try phasing
              the spectrum with just the P1 sliders. Having the pivot at the
              center will force the phases to obey: P1 = -2*P0. The center
              of the spectrum is point N/2 + 1 (e.g. point 65 of 128).

              5. If the "constrained" phases don't work, try completely interactive
              P0 and P1 phasing by the usual methods:

              i. Select one or more spectral vectors which have
              peaks over the full range of the spectrum.

              ii. Move the pivot to point to a "good" peak.

              iii. Change P0 until that peak is phased.

              iv. Change P1 until the overall spectrum is phased.

              v. Repeat (iii) and (iv) for minor adjustments if needed.

              ---
              Using NMRDraw Phase Corrections in a Script

              The phase corrections reported by NMRDraw can be used directly
              in an NMRPipe processing scheme, regardless of the pivot position
              used to phase the spectrum. You can usually simply add the P0 and
              P1 values reported by NMRDraw to the -p0 and -p1 parameters in the
              original processing script. The exception to this is if you have
              interactively re-phased an extracted (EXT) dimension with a first
              order correction. In this case, you should be sure that the phase
              correction is applied after the EXT extract in the processing scheme:

              | nmrPipe -fn EXT -left -sw \
              | nmrPipe -fn PS -p0 43 -p1 180 -di \

              ---
              Initial Delay and Phase Correction

              If a dimension is acquired with:

              No delay:
              1. No first-order phase correction.
              2. Scale first FID point by 0.5 (window -c 0.5)

              Half point delay:
              1. 180 first-order phase correction (Usually -90,180)
              2. Don't scale first FID point (window -c 1.0)

              One point delay:
              1. 360 first-order phase correction (Usually -180,360)
              2. Don't scale first FID point (window -c 1.0)
              3. Apply zero-order baseline correction to spectrum
              (POLY -auto -ord 0)
            • Keith G Inman
              Frank: I have not been able to change the pivot point by using the mouse right button in border. That has the effect of raising or lowering the display of the
              Message 6 of 7 , Aug 5, 1999
                Frank:

                I have not been able to change the pivot point by using the mouse right
                button in border. That has the effect of raising or lowering the display
                of the vector on my screen. I am viewing a 2D HSQC, and have chosen a
                vector using mouse/1D horizontal. Phasing was automatically put 'on' and
                appending the 1D did not help.

                Keith

                On Thu, 5 Aug 1999, Frank Delaglio wrote:

                > From: Frank Delaglio <delaglio@...>
                >
                > Some notes and tips on phasing:
                >
                > ---
                > Interactive Phasing
                >
                > NMRDraw will automatically reconstruct imaginary data as needed,
                > so it is always possible to interactively rephase any 1D spectral
                > vector being viewed, from any dimension:
                >
                > 1. Use "1D/1D Vertical", "1D/Z-Axis" etc to activate 1D viewing mode.
                >
                > 2. Use the mouse to select a 1D vector of interest.
                >
                > 3. Click the "Phase" button in the command "On" to activate
                > interactive phasing.
                >
                > 4. Use the "P0" and "P1" sliders or text entries to adjust the phase as
                > needed.
                >
                > Note that in any 1D viewing mode, when the mouse pointer is outside
                > the 1D viewing area in the bottom or right border, dragging with
                > the rightmost mouse button will change the position of the phase pivot
                > point. The position of the pivot will be indicated on the 1D display
                > by arrows. The pivot shows the position in the spectrum whose phase
                > will stay fixed as P1 is adjusted.

                *********************************
                * K.G. Inman *
                * Graduate Student *
                * Biochemistry/Weber Lab *
                * U of MD School of Medicine & *
                * U of MD Baltimore County *
                * Lab: 410-706-4353 -0458 fax *
                * NMR Center: 410-706-6085 *
                * Personal: 410-258-7538 *
                *********************************
              • Frank Delaglio
                Dear Colleagues, As Keith noted, I am an idiot. When I said use the rightmost mouse button to adjust the pivot point, I actually meant that other rightmost
                Message 7 of 7 , Aug 5, 1999
                  Dear Colleagues,

                  As Keith noted, I am an idiot.

                  When I said use the "rightmost mouse button" to adjust the
                  pivot point, I actually meant that other rightmost button,
                  which everyone else knows as the "Left Mouse Button".

                  The actions of the buttons are however properly listed
                  at the top border of the NMRDraw screen when a 1D view
                  mode is active:

                  Outside: [Phase Pivot] [Scale] [Offset]

                  Many apologies for my mistake.
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