Tutorial: Extract binding isotherms from unprocessed Agilent (Varian) FID

The example is a titration example of Varian format.

In each folder (e.g. 1.fid), there are just 4 files, which are fid, log, procpar, and text, which are not processed.

1. (optional) make X axis file

create an x-axis.conc using any text editor in the following format:


2. Do PCA on FID series

  • Launch trendmaingui, press Browse button of dir textbox to select all folders.
  • Note don't change file textbox as in the A simple example because the Agilent and Topspin data formats are directories, while file is used to choose single files.
  • Set type as agilentfid, scaling as auto, xunit as equivalence, and read x-axis.conc file using xaxis text box. For the FID data, solventfilter could be applied to suppress solvent peaks. Here the default Gaussian is used.
  • Press the 'Start' button, the html report will be generated if report option is turned on.

3. Reconstruct Agilent FID using only the first component

  • Luanch and run trendreconstructgui using default parameters,
  • A subfolder named as reconst (which is defined by the output option) is generated. The subfolder contains the reconstructed FID series with the same names of input files. They can be processed as the normal Agilent FID data.
  • The original 1.fid has the spectrum as (processed by NMRPipe):
  • The reconstructed 1.fid has a similar but different spectrum (processed by NMRPipe using the same NMRPipe scripts).
  • You can also visualize the reconstructed FIDs directly by choosing export format as PNG.
  • Then a series of PNG images named as reconstX.png will be generated. For example, reconst1.png is shown as:

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