NAME

pipe2flx - NMRPipe to Felix compatible data translator

SYNOPSIS

"pipe2flx -in [pipe file] -out [felix.mat file]" or "| pipe2flx -out [felix.mat file]"

DESCRIPTION

pipe2flx is a simple translation program that converts the final results from NMRPipe to a Felix compatible format. It can either be usedby stating the in-file name (NMRPipe) or by directly piping the data intopipe2flx.

Several flags have been implemented:

-in [filename]

Indicates the input NMRPipe filename. If this flag is missing, pipe2flx assumes that all data will be entered through stdin.
-out [filename]
Indicates the output felix.mat filename. This must be present for pipe2flx to run.
-verb
pipe2flx normally runs silently. -verb will have pipe2flx give updates on the current translation state. This may interfere with NMRPipe's -verb flag, so it is a good idea to have only one program in the verbose mode.
-ov
The -ov (overwrite) flag will allow pipe2flx to write over the given -out filename.
-help
This brings up a short instruction set like this one.
-felixheader
When this flag is given with a "-in (felix.mat)" filename, pipe2flx outputs the felix header and exits. This was mostly used for the debugging process, but proved useful enough to stay in the final program.
-pipeheader
Much like the -felixheader flag, when the flag is given with a "-in (pipefile)" filename, pipe2flx outputs the NMRPipe header and exits.

DIAGNOSTICS

The error messages can be quite cryptic and is something that will be improved in later versions.

BUGS

None currently reported.

NOTES

If the spectra given to pipe2flx does not have dimensions that are a power of 2, pipe2flx will fill the remaining specra in with zeroes. Thisis because the Felix submatrix format requires that the dimensions must be a power of two. A simple way to insure that this is happening (as long as a portion of the spectrum is not extracted later) is by adding the -auto flag whenrunning the ZF (zero fill) function in NMRPipe. This will at least double the data size and round up to the nearest power of two.

Future improvements will include a -chifit flag to prepare macros for use with Chifit, a better error handling system.

SAMPLE MACRO

This is a very simple 3D NMRPipe macro, not including any real data processing, to demonstrate how to use pipe2flx.

#!/bin/csh

#
# Bruker DMX Conversion: fhsqc 101097.wu

bruk2pipe -in ./ser  -noswap -DMX -decim 16 -dspfvs 10                 \
  -xN              2048  -yN                56  -zN               112  \
  -xT              1024  -yT                28  -zT                56  \
  -xMODE        Complex  -yMODE        Complex  -zMODE        Complex  \
  -xSW        10000.000  -ySW         3787.879  -zSW         1785.714  \
  -xOBS         500.132  -yOBS          50.684  -zOBS         125.763  \
  -xCAR           4.706  -yCAR         117.733  -zCAR          43.335  \
  -xLAB              1H  -yLAB             13C  -zLAB             15N  \
  -ndim               3  -aq2D          States                         \
  -out fid/test%03d.fid -verb -ov

xyz2pipe -in fid/test%03d.fid -x -verb                  \
| nmrPipe -fn ZF -auto                                  \
| nmrPipe -fn FT                                        \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di                    \
| nmrPipe -fn TP                                        \
| nmrPipe -fn ZF -auto                                  \
| nmrPipe -fn FT                                        \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di                    \
| pipe2xyz -out ft/data1%03d.ft2 -y

xyz2pipe -in ft/data1%03d.ft2 -z -verb                  \
| nmrPipe -fn ZF -auto                                  \
| nmrPipe -fn FT                                        \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di                    \
| pipe2xyz -out ft/data2%03d.ft3 -z

xyz2pipe -in ft/data2%03d.ft3 -x -verb                  \
| pipe2flx -out test.mat -ov