DATASETS

DATASET FORMAT

ADD DATASETS

MANAGE DATASETS

DATASET Parameter File

parameter file and interpret any commands therein that set parameters such as sweepwidth or spectrometer frequency. These will override any values specified in the file header. If NMRView fails to interpret the file type it then attempts to open the parameter file. If the appropriate parameters are present describing the number of dimensions, dimension sizes and block sizes NMRView will be able to read most any block structured file. Varian files can only be read correctly if they are two-dimensional phasefiles. Although VNMR (Varian, Inc.) files can be read directly, though the VNMR format is not optimal for use in NMRView. It is better to convert them to a block structured format that is prefered by NMRView. A program that does this conversion is available. If you are using FELIX to generate the matrix you can reference the dataset and set the axis mode to ppm. Also give meaningful names to the label used for each axis as these labels determine cursor tracking and peak display. Alternatively, you can leave the matrix unreferenced and enter the referencing information in a parameter file. If your are using the program nmrPipe to process datasets you can use the program pipe2nv to convert them to an NMRView compatible format. This program is a modification of Frank Delaglios pipe2xyz program.

Add

Use the "Add" command from the "Datasets" menu on the NMRView control panel to open one or more existing dataset(s). A popup window will appear that allows for interactive file selection. The scrolling display on the left lists directories, that on the right lists files. Files may be selected and opened as described below.

OK
Click SELECT on this button to open the file that is currently highlighted in the Files list. After the file is opened the panel will close.
Filter
Click SELECT on this button to select the directories and files that are displayed according to the entry in the Filter box. In the example, this results in only files ending in the directory "/home/johnsonb/data/mtx/mats" that end in ".mat" being listed in the Files list.
Cancel
Click SELECT on this button to close this panel without opening any additional files.
Select
Click SELECT on this button to open the file whose name is currently highlighted in the Files list. The panel will not close so additional selections can be made.

Manage

Use the "Manage" command from the "Datasets" menu on the NMRView control panel to display a popup window that lists all datasets that are currently opened. Datasets can be closed by seleting the desired filename and clicking SELECT on the "Delete" button. This command is useful if you want to force NMRView to reopen a particular file, perhaps after changing the reference data in the file header using an external program such as FELIX.

Close
Click SELECT on this button to close the panel.
Delete
Click SELECT on this button to delete the file from the current NMRView session. The file is not deleted from disk.

DATASET Parameter File

When NMRView opens a spectral dataset it also attempts to open an associated parameter file. It looks for a file of the same name as the dataset, but with the extension .par. For example, if the dataset is named "noesy.mat", it will look for a parameter file named "noesy.par". If the dataset is simply named "noesy", it will also look for "noesy.par". If the dataset is in the FELIX format the parameter values in the .par file will override the parameters specified internally in the .mat file. The parameter file consists of a series of lines, each one consisting of a keyword followd by one or more parameters. The keywords are as follows.
header fileHeaderSize blockHeaderSize
The header sizes must be specified if the file is not declared to be a FELIX or VNMR file. A generic description of some NMR data files is as follows: 
  fileHeader
  blockHeader1
  dataBlock1
  blockHeader2
  dataBlock2
  .
  .
  .
  blockHeaderN
  dataBlockN
The size of the fileHeader (in bytes) is specified with the fileHeaderSize parameter. The size of the blockHeader (in bytes) is specified with the blockHeaderSize parameter. One or both of these values may be 0. For example, a file may have a 16384 byte fileHeader, and no blockHeaders. This would be described as

header 16384 0

Or a file may have both, for example with a 32 byte fileHeader and a 28 byte blockHeader

header 32 28

felix
Specifiy that the file has the format used by the program FELIX. NMRView will attempt to extract the file attributes and referencing information from the header. The current version of NMRView should automatically determine if files are in the FELIX format so this should not be necessary.
vnmr
Specifiy that the file has the format used by the program VNMR. NMRView will attempt to extract the file attributes and referencing information from the header. NOTE: It is really more efficient (of memory use) to convert VNMR files to a better format. The current version of NMRView should automatically determine if files are in the VNMR format so this should command not be necessary.
dim nDim size1 blockSize1 ... sizeN blockSizeN
Specifiy the number of dimensions in the file (1-4). The size parameters specify the number of datapoints along each dimension. The blockSize parameters specify the number of datapoints in each block for each dimension. For example, a 2D file with 1024x1024 points and 64x64 points in each block would be specified as:

dim 2 1024 1024 64 64

sw dimNum sweepWidth
Set the sweepwidth for dimension dimNum to sweepWidth. Dimensions are specified as an integer from 1 to 4.

For example,

sw 1 6000.0

sf dimNum specFreq
Set the spectrometer frequency for dimension dimNum to specFreq. Dimensions are specified as an integer from 1 to 4.

For example,

sf 1 599.4

reference dimNum refPPM refPT
Reference dimension dimNum to a chemical shift of refPPM at dataset point refPT. Dimensions are specified as an integer from 1 to 4.

For example,

reference 2 4.73 513

label dimNum label
Set the label used for dimension dimNum to label. Dimensions are specified as an integer from 1 to 4.

For example,

label 3 15N