Yes, I use nmrPipe and no I do not un-transpose my data. I guess I could
do this though if that is the problem. My processing scripts are usually
derived from the default NMRDraw scripts and go something like this:
#!/bin/csh
#
# Basic 2D Phase-Sensitive Processing:
# Cosine-Bells are used in both dimensions.
# Use of "ZF -auto" doubles size, then rounds to power of 2.
# Use of "FT -auto" chooses correct Transform mode.
# Imaginaries are deleted with "-di" in each dimension.
# Phase corrections should be inserted by hand.
nmrPipe -in test.fid \
| nmrPipe -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 22.00 -p1 0.00 -di -verb \
| nmrPipe -fn EXT -x1 7.5ppm -xn 9ppm -sw \
| nmrPipe -fn BASE -nw 2 -nl 0% 5% 95% 100% \
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.5 -end 1.00 -pow 1 -c 0.5 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 0.00 -p1 0.00 -di -verb \
-ov -out test.ft2
> Hi Magnus, David,
>
> To be honest, I've never noticed this (and I haven't heard it mentioned)
> so I don't think it has ever been brought to our attention. I have an
> inkling as to what might be going on:
>
> Here in the lab we always process our data using Azara, but I hear NMRPipe
> from David - and from Magnus too?
>
> Azara will always produce spectra with the acquisition dimension along X,
> and each subsequent indirect dimension (counting back) on Y, Z, Z2 etc. It
> is my understanding that pipe will switch axes for processing and may not
> switch them back unless you say as much. I guess that in Analysis we take
> the pipe ordering to be the way that the user actually wants his/her data
> and so present it like that (with dimensions swapped).
>
> When processing with pipe, do you un-transpose your data after processing
> the indirect dimension? I'm not sure of the pipe commands, but if you
> could send one of your HSQC scripts (no need for the data) then I can have
> a try for myself.
>
> It could be that I'm wrong or that I have missed the point, but it does
> seem coincidental that we don't ever see this with Azara (and do not
> habitually use pipe).
>
> Thanks,
>
> Dan
>
> On 8 Aug 2010, at 11:35, David Langelaan wrote:
>
>> Hello,
>>
>> I have noticed the same behavior as well. To be honest, I didn't figure
>> out how to change this setting in Analysis. I use NMRPipe to process my
>> files and my work around was to add a second transpose command at the
>> end of the processing script.
>>
>> David
>>
>>
>> On 8/7/2010 6:17 AM, Magnus Kjærgaard wrote:
>>> Hi all...
>>>
>>> This is probably something that has been covered before but it annoys
>>> me
>>> on a daily basis, so I'll take it up again. When a 2D experiment is
>>> opened, (say a 15N HSQC) the heteronuclei dimension ends up on the
>>> X-axis
>>> and hydrogen ends up on the Y-axis in the window that is automatically
>>> opened. Any NMR spectroscopist I know would want it the other way
>>> around.
>>> I realize that I can change the axes in the Window dialogue, however
>>> this
>>> takes almost 10 seconds of my precious time :-).
>>>
>>> Would it be possible to change the default behaviour to automatically
>>> put
>>> H on the X-axis an 15N on the y-axis? Alternatively, in case other
>>> people
>>> are strongly opposed to this, would it be possible to have a "User
>>> preferences" option that determined what ends up where?
>>>
>>> Magnus Kjaergaard
>>> University of Copenhagen
>>>
>>>
>
> Daniel O'Donovan
> [log in to unmask]
>
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