| cf {rNMR} | R Documentation |
GUI for converting Bruker, NMRPipe, or Varian format files to UCSF (Sparky) format for use in rNMR.
cf()
cf displays a GUI for converting spectra. cf supports
processed one-dimensional or two-dimensional Bruker, Varian, NMRPipe, or
ASCII (see ca) format files. To convert files, set the input
directory using the Browse button. This directory should contain
folders for the spectra being converted or the folder for the spectrum
itself (see "File Structure" below). Press the button corresponding to the
file type for conversion (Bruker, Varian, NMRPipe, or
ASCII) to display the appropriate folders contained within the input
directory. Select the files you wish to convert from the files list and then
press the Next button.
For Bruker and NMRPipe files, this will bring up a dialog containing the selected spectra as well as the corresponding output names for the newly converted files. Checking the 1D Drift correction box will correct DC offset problems and set the median noise level to zero. Once the conversion parameters have been set, press the Convert button to convert the displayed files to UCSF (Sparky) format.
For Varian files, the dialog will contain an additional column indicating the indirect nuclei for the selected spectra. By default, the conversion function selects the indirect nucleus using the "dn" parameter from the spectrum's "procpar" file. If this value is incorrect, multiple entries may be edited simultaneously by selecting the appropriate files from the list, and then selecting the desired nucleus from the drop-down box at the bottom of the dialog. This step is only necessary for 2D spectra, as the "tn" (transmitter nucleus) parameter from the "procpar" file is always the correct nucleus for the direct dimension. For arrayed 1D experiments, each dataset in the array will be saved as a separate spectrum and will be numbered sequentially (appended to the output name).
rNMR's file converter assumes a certain file structure for input directories which must be adhered to for file conversions to be successful. Bruker format spectra must contain processed data files ("1r" or "2rr") in a folder named "pdata". This folder must also contain the processing parameter files ("proc", "procs", "proc2", or "proc2s"). Acquisition parameter files ("acqu", "acqus", "acqu2", or "acqu2s") must be in a directory above the "pdata" folder. These files/folders may be nested within other folders, so long as a "pdata" folder exists somewhere in the spectrum's directory.
NMRPipe format spectra should be individual files containing the NMRPipe format header for the spectrum followed by the processed data. These files should have a ".ft2" or ".dat" extension.
Varian format spectra must contain a processed data file ("phasefile") as well as a processing parameters file ("procpar"). The processed data must be in the directory for the spectrum or in a folder named "datdir". When a spectrum is saved in Vnmr, the processed data file is not written to the same location as the saved spectrum. Instead, "phasefile" is saved to Vnmr's default experimental directory (e.g. "~/vnmrsys/exp/datdir/phasefile"). Spectra may be converted from the "vnmrsys" directory or from the directory where the spectrum was saved, as long as the "phasefile" and "procpar" files are present. These files can be copied automatically for multiple spectra using the Vnmr macro provided at the rNMR website, (http://rnmr.nmrfam.wisc.edu/pages/download/export.html). For details on changing the processing commands within the macro or for instructions on copying "phasefile" and "procpar" manually, refer to the "Varian processing requirements" section below.
The "phasefile" and "procpar" files can be copied manually from the "vnmrsys" directory to the saved directory for the spectrum if the spectrum is processed correctly. To ensure proper conversion in rNMR, Varian spectra must be processed using the following commands:
fn=np*2 ft f full vsadj dc ds flush
fn=np*2 ft f full vsadj dc dssh flush
trace='f1' wft2da f full dconi flush
These commands can be altered, but there are a few restrictions. The "ft" and "wft2da" commands can only be substituted with equivalent Fourier transform commands. Alterations to the processing parameters (e.g. zero filling, window functions, phasing) must precede the Fourier transform command. For 2D spectra, "trace" must be set to "f1" directly before the data is transformed. All commands listed above that follow the Fourier transform command are required. And finally, for arrayed 1D experiments, the "dssh" command is necessary to display the full array.
Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu
ca for converting ASCII (plain text) files;
rNMR for other rNMR help topics.