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Notes on XWINNMR Contents
 

Notes on XWINNMR

Marc Guenneugues

Jun  9, 1999

Xwinnmr is the software developped by Bruker to monitor their spectrometer (acquire, process and analyse NMR data). It is available on every Bruker spectometer of course, but also on any worstation since the group acquired two floating licenses. The present document is a short and gentle introduction to this program.




 
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Contents

1  File system organisation
2  Useful commands
3  Some parameters


 
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1  File system organisation

Unlike other NMR dedicated softwares 1, XWINNMR enables you to work directly where the files are stored. This offers some flexibility but is also relatively unsafe for the data2. This is counterbalanced by a strict hierarchy in the filesystem.

  • The software is located in /u/prog
  • The configuration files defining the hardware to pilot are in /u/conf
  • Plotting peripherals are in /u/plot
  • Printing peripherals are in /u/print
  • Files necessary to handle an experiment are in /u/exp, and more precisely in the case of NMR (Bruker builds other instruments types) in /u/exp/stan/nmr

    • The par subdirectory contains referenced parameters to run specific experiments
    • The lists subdirectory contains all the necessary files used to run the experiements

      • pp : pulseprograms
      • cpd : composite pulse sequences for decoupling
      • gp : gradient programs (not available on the AMX360)
      • wave : files defining the shape for soft pulses
      • bsms : shim setting files
      • f1 : frequency lists
      • roi : region of interest files (used upon 2D integration for instance)
      • mac : user-defined macros

  • Recorded data are stored in /u/data, and more precisely in
    //data//nmr, where du is the disk unit (either /u or /v in the present case) and user is the login name (nmr1 in the present case). A dataset is defined as a subdirectory. The given name should be explicit3. The dataset may consists of several experiments defined as subdirectories labelled with an integer. Inside this directory, one finds several files :

    • acqun (n is nothing or an integer) containing the acquisition parameters ( acqu for the acquisition dimension, acqun for the indirect dimensions). These files are updated each time a parameter is modified.
    • acquns containing the effective acquisition parameters when an experiment was run4.
    • fid (for a 1D experiment) or ser (for a multidimensional experiment) containing the recorded free induction decays.
    • a subdirectory pdata where will be located the processed spectra. It is possible to do different processing to some recorded data. Each processed spectra will be located in a subdirectory labelled by an integer. Inside these subdirectories, one finds

      • procn and procns which are files equivalent to acqun/acquns but for the processing parameters
      • title containing the title of the run experiment (if set using setti)
      • files containing the spectra (1r, 1i for a 1D spectrum ; 2rr, 2ri, 2ir, 2ii for a 2D spectrum ;...)
      • files used for the display
      • files containing specific informations (integral values, ...).

One can access a specific dataset by two ways

  • Typing edc will popup a graphical menu where one enters the required information (the dataset name, the experiment number (referred to as expno), the processed number (referred to as procno), the disk unit, the user name, the experiment type (nmr in all instances)).
  • Typing re [dataset name]5expno [procno]

Within an experiment, one can access a new processing cluster typing repprocno.

Note that edc is also a way to create a new dataset by entering a new name or expno.


 
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2  Useful commands

  • Define working datasets

    • edc (previously described)
    • re/rep (previously described)
    • edc2 : similar to edc but to define the secondary dataset used to perform 1D dual display (spectra overlays)

  • Store data

    • wra [dataset name] expno : copy the acquisition data to the new experiment block
    • wrp [dataset name] [expno] procno : copy the processed data to the new processing block
    • wrpa [dataset name] expno [procno] : copy the acquisition and processed data to the new experiment block
    • wpar [dataset name] : copy parameters (acquisition, processing, display, plot) to a backup place

  • retrieve data

    • rpar [dataset name] : copy parameters from a backup place

  • edit parameters in a working dataset

    • edcpul : edit current pulseprogram
    • edgp : edit gradient program
    • edlist fxname : edit frequency list number x with name name
    • parameter value : assign a value to a specific parameter
    • eda : edit acquisition parameters (modifies files acqun)
    • edp : edit processing parameters (modifies files procn)

  • preacquisition

    • edasp (DMX only) : define the amplifier routing
    • wobb : start the wobbling mode for tuning/matching the probe
    • rsh : retrieve shim settings
    • wsh : store shim settings
    • gradshim (DMX only) : start the automatic gradient shimming procedure

  • acquisition

    • lockdisp : start the lock display window
    • acbdisp (DMX only) : amplifier control display window
    • pulsdisp (DMX only) : pulse program analyser (fully detailed)
    • ppg (DMX only) : pulse program analyser (overview)
    • stdisp (DMX only) : shape tool module
    • acqu : switch to the acquisition mode
    • expt : compute the experiment duration
    • rga : estimate the optimal receiver gain
    • gs : start an interactive aquisition mode enabling the proper setting of parameters
    • zg : start an experiment
    • stop/halt : stop an experiment
    • ii : initialize interfaces

  • processing

    • em : apply exponential mulplication
    • sinm : apply sinus multiplication
    • ft : 1D Fourier transform
    • trf : 1D user-defined Fourier transform
    • pk : apply phase correction (according to previously set parameters)
    • apk : 1D automatic phase correction
    • xfb : multidimensional Fourier transform
    • abs2/abs1 : polynomial baseline correction (acquisition/indirect dimension)

  • about plotting

    • edg : edit plot parameters for current experiment
    • edo : edit output device for plotting and/or printing
    • plot : plot the current spectrum


 
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3  Some parameters

Parameters are accessed via the command [n[s]] parameter [value] where n[s] indicate the dimension it is applied to (when omitted it applies to the acquisition dimension).

  • acquisition

    • pulprog : pulse sequence
    • grdprog : gradient program
    • fqnlist : frequency list n
    • ns : number of recorded transients to enhance the signal to noise ratio and/or perform the correct coherence selection
    • ds : number of dummy scans performed in order to reach the steady-state conditions
    • aq : acquisition time
    • td : number of points
    • sw/swh : spectral width (in ppm/Hz)
    • sfon [1..8] : frequency for channel n (depends on the studied nucleus)
    • nucleus : defines the studued nucleus
    • pn [0..31] : pulse lengths
    • dn [0..31] : delays
    • hln [1..4] (AMX only) : power level of the transmitter line
    • dln [0..7] (AMX only) : power level of the decoupler line
    • dbln [0..7] (AMX only) : power level on the second decoupler line
    • pln [0..31] (DMX only) : power level n
    • spn [0..15] (DMX only) : power level for shape pulse n
    • spnamn [0..15] (DMX only) : shape filename for shape pulse n
    • spoffsn [0..15] (DMX only) : frequency offset for shape pulse n
    • ln [0..31] : loops

  • processing

    • si : spectral size
    • offset : reference shift at the extreme left side of the spectrum
    • wdw : apodization function
    • lb : line broadening (for an exponential multiplication)
    • gb : gaussian broadening (for a lorentzian to gaussian transformation)
    • ssb : sinebell shift (for a sine/qsine window)
    • tdeff : used points in the Fourier transform
    • tdoff : number of points unused at the start of the FID
    • phc0 : constant phase correction
    • phc1 : linear phase correction
    • absf1 : lower limit for spectral analysis
    • absf2 : upper limit for spectral analysis


Footnotes:

1 See VNMR for example

2 That means that proper backups should be performed.

3 reminding the sample and/or the run experiment and/or the date

4 These are thus the files to check when the experiment is finished !

5 Items enclosed with [] are optional.


File translated from TEX by T TH, version 2.27.
On  9 Jun 1999, 10:24.