Thank you to everyone (Dave, Martha, Josh, Pierre, Steve, Lawrence, Mike,
and Alan – sorry if I missed someone) who responded to my question of
converting Bruker data to Varian. It was very helpful.
Many people suggested the convertbru and sread commands in VNMR, and a
couple people gave me all of the flags that have to be set to get it to
work correctly.
I was able to do it with a combination of the information from Steve
McKenna and Alan Kenwright.
Apart from using third party software, the procedure appears to be:
1. On the Bruker, use
convdta expno
to convert the digital data to analog and save it to a new experiment
number (expno)
2. Transfer the data directory using your favorite FTP software or mounted
disk.
3. On the Varian, use
convertbru('brukerfile/expno','-bamx','-ctempfile.cv')
where tempfile.cv is a temporary file that is created
If you left the data in digital mode, you need to add a –omsb flag in the
convertbru command:
convertbru('brukerfile/expno','-bamx','-omsb','-ctempfile.cv')
4. Read the file in with
sread('tempfile.cv','template.par')
where ‘template.par’ is either a parameter set you have created, or there
is a default bruker.par folder in the parlib directory. I used:
sread(‘tempfile.cv’,’/export/home/vnmr/parlib/bruker’)
I got an error if I specified bruker.par, but dropping the extension
worked.
If you do not convert the data from digital to analog, you have to figure
out how many points to left shift the data on the Varian, and there will be
a subsequent first order phase correction to apply. Steve tried it both
ways, and he reports some small wiggles at the baseline when the data is
converted to analog first. I have not had time to play around to see what
sort of impact this has on integration.
It loses some things like spectral referencing and the text file, but those
are minor adjustments. The people that do this often have macros to make
sure the little details and parameters are moved over correctly.
Below are the raw responses from everyone.
Thanks,
Ben
Benjamin G.M. Chew, Ph.D.
Manager
Analytical Services and Technology
Ashland Inc.
5200 Blazer Parkway
Dublin, OH 43017
614-790-6809
614-790-4294 (fax)
bchew_at_ashland.com
______________________________________
Check out the Varian command 'convertbru'
There is an analogous Bruker command 'vconv'
As a business matter, they each import the competitor's data, they don't
make it easy to export their own ...
____________________________________
Why not go the other way? The old command on Varina is bru2var and is in
the liquids manual. I can look this back up, if no one else replies. You
can
do a Vconv in Topspin 1.3 (not sure about 1.2). Use file open other data,
use tab to select Varian.
___________________________
I haven't done this myself, but there may be a way to do this with the
program NMRPipe. If includes scripts to convert varian and Bruker
format data to NMRPipe format. It might have scripts to go back the
other way as well, enable you to do your conversion in a two-step
process.
____________________________
From vnmr command line, you can use convertbru. (see "VNMR command and
Parameter Reference" documentation)
I do not know any software on PC, but it should not be complicated to
program an au program to do that in topspin.
_____________________________
We do this with Avance data. VNMR comes with a program convertbru which
does this. From the VNMR command line, you would enter:
convertbru('brukerfile/1','-bamx','-omsb','-ctempfile.cv')
...where brukerfile is the data (copied to the Sun, or NFS-mounted); 1,
2, etc. is the Bruker experiment number; and tempfile.cv is a temporary
directory that convertbru will create. It will be in Varian's old sread
format. To retrieve it into VNMR, do:
sread('tempfile.cv','template.par')
You will need to prepare template.par in advance; it is a parameter set
in VNMR format which is used to provide defaults for any parameters
convertbru couldn't get from the Bruker file. Any normal 1-D parameter
set will work for starters, and you can customize it from there. Once
you have the data in VNMR, you can use the svf command to save it in
VNMR format.
Some parameters still don't transfer well. We use a macro full of
commands like setvalue('tn','H1','processed') to set some parameters
that come in with weird values. Also you will have to left-shift
digitally filtered data by ~50 points or you will need a very large left
phase. I can send the macro for all this if you like.
_____________________________
Try contacting Virginia Miner of Acorn NMR at gina_at_acornnmr.com. Acorn's
NUTs NMR data processing software will get the job done for you.
_______________________________
Have you looked at "convertbru" and "sread" in vnmr? There
are a
few words here:
http://www.chem.wisc.edu/~cic/nmr/Guides/BAVUG/AVANCE_to_VNMR.pdf
______________________________________
We do the conversion of Avance/Xwinnmr data to VNMR6.1C here on a
routine basis using a combination of "convertbru", "sread" and some
custom macros originally written by Gareth Morris at Manchester and
tweaked here to our particular needs. I'm not certain that the data
format under Topspin 1.2 is the same as under Xwinnmr, but I would hope
so (otherwise Bruker have dug themselves a very deep hole!). We do it at
the Sun end on the fly (the machine works out that the file it is
loading is Bruker data rather than Varian and automatically performs the
conversion). The only slight problem is sorting out the digital
filtering on the Bruker. I have found that the easiest thing is
actually to convert the Bruker data to analogue format first (using
CONVDATA), but if all the files you want to convert are similar (say all
proton spectra run under fixed conditions of spectral width, etc) you
can fix it at the Varian end instead using lsfid and a 1st order phase
correction.
If you don't find exactly what you are looking for (ie a package to do
it at the Bruker end) and would like to implement something similar to
what I have outlined get back to me and I'll sort out a package of the
necessary files - as usual with these things there is some string and
chewing gum and a bit of spaghetti logic involved, but it should be
possible to sort out a coherent package and comment it so that all is
clear.
If you're not sure about the Bruker file format and would like to try
one before committing, just tar or zip a Bruker data file (the whole
directory rather than just the acqu file or whatever) and email it to
me. I'll run it through one of our data stations and let you know the
outcome.
__________________________
bchew_at_ashland.com wrote:
> Hi All
>
> I tried looking in the archives, but was unsuccessful.
>
> I would like to convert 1D Bruker (AVANCE, Topspin 1.2) data to Varian
> (VNMR 6.1C) format. Does anyone have or know of a program that can do
> this?
> I would prefer to run it on a Windows format (on the Bruker instrument),
> but in a pinch, I can transfer the directories to the SUN (Varian) and
> run it in UNIX.
>
>
> Thanks
>
> Ben
>
______________________________________________________________________
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Received on Wed Feb 08 2006 - 09:56:19 MST