Converting NMRPipe to other formats

To nmrview format

To convert to nmrview 2D format:
pipe2xyz -nv -out hsqc.nv < test.ft2

For nmrview 3D spectra:
xyz2pipe -in ft/test%03d.ft3 | pipe2xyz -nv -out newcbca.nv

To SPARKY format

2D data

From a computer on which Sparky is installed, issue this command:

pipe2ucsf data_pipe data_sparky

"data_pipe" is a single file that contains the 2D processed nmrPipe spectrum, and "data_sparky" is the file that contains the Sparky spectrum to be created.

For 3D data, which is pretty much the same as using cat to put everything together

xyz2pipe -in ./hcch%03d.DAT -x > hcch3D.ft

pipe2ucsf -<axis order> hcch3D.ft spectrum_ucsf

The <axis order> parameter is the same as the "order" parameter in nmrDraw, its value can be read by selecting the "parameters" button under "file" in nmrDraw menu. For example, order is "2 1 3" in nmrDraw, then use:

pipe2ucsf -213 hcch3D.ft spectrum_ucsf

An order describes the order in which the time variables in the various dimensions are acquired in an experiment. For example, an order of " 2 1 3" means that t3 was acquired first, followed by t1 increments, and then by t2 increments.

To XEASY format

I have not used this extensively. Only for a couple of nadeem's 3D spectra but it does work

I use the programme pipe2xeasy (complied for both linux and sgi's).

I simply tagged the following at the end of the nmrPipe processing file:

e.g. nmrPipe -di | pipe2xeasy -f factor -out xeasy_file


Here is an example: the line for conversion is highlighted
the output files are (in this case) cco.3D.param and cco.3D.16
Note the data must be in real format or you get garbage

For the -f value you will need to do a few trial runs.


#!/bin/csh

#
# 3D States-Mode HN-Detected Processing.

xyz2pipe -in fid/test%03d.fid -x -verb \
| nmrPipe  -fn SOL                                  \
| nmrPipe  -fn SP -off 0.35 -end 0.98 -pow 2 -c 0.5  \
| nmrPipe  -fn ZF -auto                             \
| nmrPipe  -fn FT                                   \
| nmrPipe  -fn PS -p0 69  -p1 0.0 -di               \
| nmrPipe  -fn EXT -left -sw                        \
| nmrPipe  -fn TP                                   \
#| nmrPipe  -fn LP -fb          \
| nmrPipe  -fn SP -off 0.35 -end 0.98 -pow 2 -c 0.5  \
| nmrPipe  -fn ZF -auto                             \
| nmrPipe  -fn FT                                   \
| nmrPipe  -fn PS -p0 90 -p1 0 -di              \
| nmrPipe  -fn REV                                   \
| pipe2xyz -out ft/test%03d.ft2 -y

xyz2pipe -in ft/test%03d.ft2 -z -verb               \
#| nmrPipe -fn LP -fb                                           \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5  \
| nmrPipe  -fn ZF -auto                             \
| nmrPipe  -fn FT  -alt                                 \
| nmrPipe  -fn PS -p0 -20.0 -p1 0.0 -di               \
| nmrPipe -di | /ozzy/pipe2xeasy.lin -f 0.2 -out cco