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1D Acquisition and Processing

Bruker Avance AV / Topspin 2.1
print version: pocketmod (1 page) or full size (6 pages)

  1. Login and open the program
    1. Sign the logbook (name and phone number)
    2. Login to the computer
      • user name
      • password
    3. Open Topspin
      • topspin icon
  2. new window
    Create a new file the "experiment number"
    each expno file can contain one fid file called "fid" calls a set of standard parameters for
    acquisition (eda) and processing (edp)



  3. Insert the sample (sample preparation)
    tube in spinner
    1. Place the spinner into the depth measure
      Slide the tube down to the bottom (liquid level c.a. ≥ 3 fingers)
    2. Hold the tube above the spinner
      Wipe the outside of the tube and the spinner
    3. BSMS keypad (full picture on page 2):
      press the “lift on/off” (green = on)
    4. WAIT until you hear the air flow then set the spinner on the air cushion
    5. Press the “lift on/off” button (no light = off)

  4. AV300 ONLY:
    Spin
    (optional) Use the BSMS keypad:
    bsms top row
    1. Press “spin on/off” (green = on)
    2. To check the spin rate:
      press the orange 2nd button and then the
      "spin rate/spin measure" button
    3. To deselect spin rate, press: stand-by

    AV500 ONLY:
    Tune and match
    (for each nucleus and each sample)
    type: atma
    • performs automatic tuning and matching - automatically
    • or for the manual mode,
    type: atmm
    • the woble curve is displayed in the acquisition window
    • to just view the wobble curve without adjusting the tune or match,
    • type: wobb

  5. Lock
    the lock display
    1. Click lock display menu icon or type: lockdisp
    2. Read a shim file by typing:
      rsh qnp (AV 300)
      rsh bbo (AV 500)
      (or add a button to your menu bar)

      the shim file names are derived from the probe in the magnet
      the standard probe on the AV 300 = (1H, 31P, 13C,29Si qnp probe with 2H lock
    3. Click lock icon or type: lock
      select your deuterated solvent
      this sets the chemical shift reference


  6. Shim
    1. Adjust “lock phase” to maximize the lock signal

    2. Adjust the axial shim currents
      Z, Z2, Z, Z2 . . .
      until no further changes
      the bsms keypad

      light:
      “fine” “ON AXIS” “Z1

      lock signal off the screen?
      reduce lock power or lock gain or lock DC

      pressing a lit button
      will undo changes

      pressing an unlit button
      (example: STD BY)
      will save changes

    3. When not spinning adjust
      X, Y, XZ, YZ, . . .
      until no further changes

      light: “fine” “X” “Z1

      pressing “Z0
      will undo
      changes on X or Y

      pressing “Z 1
      will undo changes on XZ or YZ

    4. use gs mode to shim on the FID or the spectrum

    5. Done?
      press STD BY



  7. Parameter setup
    acquisition parameters
    1. Click the AcquPars tab or
      type: ased

    2. Type: rga
    3. click start acquisition icon or type: zg
      for a preliminary acquisition

      The pulse program “zg” is a
      single-pulse experiment.
      Type: showpp
      to see it graphically.

      The command zg starts acquisition.

      Click the PulseProg tab
      to see the Bruker code
      defining pulses, delays,
      power levels, channels, and phase

    4. Tailor the parameters
      FID, time domain
      aim: avoid clipping of the free induction decay
      x-axis: estimate the final acquisition time
      • (FID takes up ~ the screen)
      y-axis: if rga gave rg = 1, then reduce your pulse width (p1)

      Spectrum, frequency domain
      type: proc (this macro runs ft, apk, abs, ppf, .vr)
      how is the shimming?
      zoom in and check . . . do more shimming if needed (d1 0s, gs)
      Expand the region of interest to fit the screen and click set sw and sfo1 icon
      • (note: the red arrow alone changes o1 via the mouse)
      or type: .setsw
      or type in values for o1p and sw

      (to avoid measuring excess noise and to increase digital resolution)
      adjust td to get the desired aq (aq = td*dw = td/(2swh))
      adjust si=2*td to get optimal zero filling
      (note:, the smaller (Hz/pt), or (sw/si), the higher the digital resolution)
      set ns (8 for a full phase cycle)
      set ds (common value = 2)
      set d1 (depending on T1's and the desired effects)
      check the experimental time by clicking experimental time iconor typing: expt


  8. Acquire a FID
    1. play icon or type: zg
    2. Options during FID acquisition:
      • tr - saves the data and continues acquiring
      • h halt icon - HALTs the acquisition and SAVEs your FID
        • the FID is automatically saved once ns is reached
      • go - acquires more ns without deleting the stored FID
        • adds the new transients (ns) to the stored FID
      • stop - terminates the experiment – data will be lost
      • kill - terminates the experiment – data will be lost

  9. Processing
    1. ft (Fourier transform)
      automatically applies the bc_mod and me_mod specifications
      window functions can optionally be applied to the FID
      • sensitivity-enhancement (lb > 0), type: ef
      • resolution-enhancement (lb < 0, gb > 0), type: gf
      right-click to alter the display properties

    2. apk (automatic phase correction)
      Manual phase correction: type: .ph or click:
      phase icon and menu
      “0” for zero-order phase correction
      (on the largest peak; red line)
      “1” for first-order phase correction
      (on the furthest peak)
      to change the red line's position: right-mouse click (“set pivot point”)
      save and exit: .sret save and return icon

    3. chemical shift calibration icon
      chemical shift calibration
      type: .cal or click:
      place the cursor at a known position (e.g. CDCl3 = 7.26 ppm)
      click the left-mouse button to define its position

    4. Baseline correction
      Type: abs (automatic baseline correction)
      automatic integration is also performed if the parameter intbc is set to yes
      baseline correction icon
      Manual correction: .basl or click:
      click the triangle to view changes
      save and exit

    5. Peak picking
      Type: ppf (automatic peak picking)
      to toggle display units to relative: click y-axis icon or type .y
      peak pick icon
      to change parameters for peak picking, type: pp
      or type the values in the command line for mi, maxy, cy
      Manual/interactive peak picking, type: .pp
      define the peak picking range (green box)
      draw a box around the peaks to pick
      the symbol with the "m" allows you to change the box dimensions
      the peak picking icon allows you to select a single peak with the mouse
      save and exit

    6. Integration
      Type: abs (automatic integration and baseline correction)
      for automatic integration without baseline correction, absg 0 then abs
      integration mode icon

      Manual correction: .int or click:
      to delete all: “select all” with select all integrals icon and delete delete integrals icon
      to define new integrals, highlight:define integrals icon
      to calibrate an integral, with the cursor on the peak, right-click: integrals sub-menu
      save and exit

    7. Plotting
      For a simple printout of the screen, type: prnt
      To export pdf files of your plot, or have control of colors, fonts, sizes
      enter the topspin plot editor by typing: plot
      In brief, a description of the plotting elements:
      “Data” contains the list of expno's listed in the plot editor's portfolio
      The green squares icon allows data window selection
      “Edit” to change colors, fonts, displayed regions, etc.
      “1D/2D Edit” to interactively change intensity and plot region
      File, Print to get a hardcopy (control p)
      File, Export to save a picture (formats include: pdf, jpg, emf, and bmp)
      DO NOT SAVE (this changes the file called by “layout” in topspin)

  10. Save your data onto another computer
    DATA MAY BE DELETED WITHOUT WARNING
    1. Open the my computer file icon on the desktop (double-click nmr300 or nmr500)
    2. Click the “start” icon to get to the nmrlab4 network shortcut
    3. Drag and drop files from nmr200 to nmrlab4 and preserve the hierarchy: directory/data/user/nmr/name/expno

  11. Remove your sampleon the BSMS keyboard:
    1. TURN OFF: spin and lock (no light = off)
    2. press “lift on/off” (green = on)
    3. gently remove your sample from the magnet – lift it up to clear the magnet
    4. press “lift on/off” (no light = off)

  12. Log off

  13. Open your files on another computer To open Topspin files on the other computer:
    Topspin icon
    1. Open the program Topspin
    2. Navigate to your data using the Browser
    3. Drag you data file into the display window

  14. Report problems and bugs to Yael or Shifi - 3748