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.
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.
One can access a specific dataset by two ways
- The software is located in /u/prog
- The configuration files defining the hardware to pilot are in
- 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
- The lists subdirectory contains all the necessary files used to run the
- 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
- 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
- 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, ...).
- 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
Note that edc is also a way to create a new dataset by entering a new name or
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).
- 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
- 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
- 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
- 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
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.