On 10/12/10 12:10, Brian Smith wrote:
> Lack of a "varian" keyword in the par file will mess up the processing for
> sure.
In no combination the varian keyword works.
> Varian data always used to be big-endian, but that may no longer be the case
> now that they are hosted on LINUX boxes. However, I do remember that there was
> a flag in the header that specified this.
The header says:
$ var2pipe -info -in fid
LengthType: short
WordType: float
QuadType: complex
WordSize: 4
FIDSize: 1794
FIDCount: 400
ExpCount: 1
I don't get a clue from that about the endianess. But my azara is
compiled for little endianess as default. And I get some results with
that. Switching to big_endian gives bad results. I would say from that,
that my data is little.
Using the look_at it looks for me that the data is swapped, as the
output for swapped makes more sense.
> Looking at the Varian docs I guess this means that you have two or more FIDs
> stored together - is the expt a pseudo 3D of some sort?
No it is a plain gNfhsqc spectrum. Nothing special
> Rather than going via formatConverter (which I agree should be possible) you
> might find the attached script useful for creating .par and script files for
> Varian data. You probably need to change nawk to awk depending on your OS.
>
Thanks for this script, but is basically gives the same results as
formatConverter. But it also says "int", which is wrong telling from the
header. And it sets the "varian 2" which doesn't work with process.
These scripts are working, at least give me a spectrum. Never the less
the phase in the direct dimension is rolling so that a huge first order
phase correction needs to be applied.
_fid.par_
ndim 2
file /mnt/tmpfs/fid
swap
dim 1
! npts 1794 ! original number of points
npts 1801
sw 14044.9438202
sf 899.8646188
refppm 4.77299999985
refpt 513
nuc 1H !Nucleus
dim 2
npts 200
sw 2800.0
sf 91.1930195
refppm 120.271140822
refpt 258.0
nuc 15N
_process.scr_
input fid.par
output spectrum.ft
par spectrum.par
script_com 1
range 2 1801
complex
conjugate
sinebell2 60
zerofill 1
fft
phase 0 0
reduce
range 1 1024
end_script
script_com 2
complex
conjugate
sinebell2 60
zerofill 1
fft
phase 90 -180
reduce
end_script
--
Justin Lecher
Institute of Structural Biology and Biophysics
ISB-3 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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