| ca {rNMR} | R Documentation |
GUI for converting ASCII (plain text) format spectra to UCSF (Sparky) format for use in rNMR.
ca()
ca displays a GUI for converting ASCII spectra. ca supports
processed one-dimensional or two-dimensional spectra. To convert files,
designate an output directory and select files for conversion using the "Add
Files" button. Output names may be modified by clicking within the "Output
Names" column. Pressing the "Append Paths" button will append the file path
to the output name for a selected file. Checking the "1D Drift correction"
box will correct DC offset problems and set the median noise level to zero
for all one-dimensional spectra being converted. The direct and indirect
nuclei for each spectrum must be provided before conversion. The field
strength each spectrum was collected under may also be provided, but this is
optional (see the Conversion accuracy section below). Click anywhere
within the table to edit a single entry. Multiple entries may be edited
simultaneously using the options at the bottom of the GUI. Once the
conversion parameters have been set, press the "Convert" button to convert the
displayed files to UCSF format.
rNMR's ASCII file converter assumes a certain file structure which must be adhered to for conversions to be successful. Two formats are accepted by rNMR. One-dimensional spectra must include two columns, the first containing the chemical shift at each point in the spectrum and the second containing the intensity at each point in the spectrum. Any lines within a file that contain non-numeric values will be ignored during conversion. Two- dimensional spectra may be formatted in a similar matter, the first column containing direct chemical shifts, the second containing indirect chemical shifts, and the third containing intensities. Shifts need not be ordered under this format, as long as values in each row correspond to each other.
Two-dimensional spectra may also be formatted into a matrix of intensities (recommended). Each value in the matrix must be separated by tabs or whitespace. The first row of the matrix must contain the chemical shifts in the direct dimension, in ascending order from left to right. The first column of the matrix must contain the chemical shifts in the indirect dimension, in ascending order from top to bottom. The first value in the matrix (the top, left corner) will be ignored. This format allows for quicker conversion and smaller file sizes.
Both formats require that values be written in ASCII (plain text) and must be separated by tabs or white space. Files must contain data for every point in the spectrum and should not be thresholded or compressed.
UCSF format spectra produced by rNMR's ASCII converter may be opened in rNMR as well as Sparky. During conversion, rNMR appends the up and downfield shifts provided in the ASCII file to the UCSF format file header. This information is not usually included in UCSF files and is not used by Sparky when opening spectra. If you wish to open converted files in other programs that support UCSF format (such as Sparky), it is important to note that the accuracy of the chemical shifts in the converted file is dependent upon the accuracy of the field strength value provided during conversion.
Under normal circumstances, when a file is opened in rNMR or Sparky, the up and downfield shifts in each dimension are calculated using the transmitter frequencies, sweep widths, and center frequencies included in the file's header. This step is bypassed in rNMR when opening spectra produced by the ASCII converter. Instead the up and downfield shifts are taken directly from the original file in order to ensure accuracy. This is not the case when using Sparky.
The transmitter frequencies included in the UCSF header are calculated using the nucleus names and field strength values provided during conversion. This is accomplished using chemical shift referencing values available at http://www.bmrb.wisc.edu. Because these calculations are dependent on the field strength values provided, it is important to report field strengths with as much accuracy as possible. If the field strength is not provided during conversion, the UCSF file produced by the converter may only be opened and displayed accurately by rNMR.
Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu
BMRB homepage: http://www.bmrb.wisc.edu; Sparky user manual (http://www.cgl.ucsf.edu/home/sparky/manual/files.html#UCSFFormat)
rNMR for other rNMR help topics.