Hi all:
As so often happens with the AMMRL group, I received a quick and large
response to my question about TopSpin data imports of Varian data. Many
thanks to:
John Harwood, Pat Stone Wilkinson, Roberto Gil, Dave Scott, Josh Kurutz,
Brian Cherry, Mike Engelhardt, Markus Heller, Paul Cope, Clemens Anklin,
Kelly Moran, Rich Shoemaker, Tim Flood, Jerry Hu, Martha Morton,
Christian Schorn, Feng Qiu, Greg Heffron, Andy Soper, Joe Ray, James
Hook, Hamish Grant, David Grace, Andy Edwards, and Anne Gorham.
for their very helpful comments!
Summarizing those responses:
TopSpin imports Varian data without any serious problems. A wide range
of researchers are doing this on a regular basis. 'vconv' converts the
data to a Bruker dataset which is then processed in the normal fashion.
MC2 may need to be adjusted for certain types of 2D datasets (to match
the acquisition mode for the indirect dimension). Mike Engelhardt has
written to the group as to how to correct for this: make up a parameter
set named the same as the Varian pulse sequence and having the correct MC2.
Often mentioned was Bruker's recent announcement of $99 pricing for a
student edition of TopSpin (which initiated the interest here).
A listing of the anonymized responses is provided below.
Cheers,
Charlie
******** original email ************
Charles G. Fry wrote:
> Hi all,
>
> I have had some students recently asking me questions about TopSpin
> (e.g., postdocs that have used it elsewhere). In particular, they want
> to know whether the software can import Varian data sets.
>
> I have not used TopSpin, but have imported Varian data into XwinNMR in
> the past with varying success. It would be helpful to hear from any
> TopSpin users out there in AMMRL land that import Varian spectra how
> well that works for you.
>
> Cheers,
> Charlie
>
*** RESPONSES ***
1************************************
I use TopSpin 2.1 to process Varian VNMR data regularly. Works fine.
Also Bruker has just released a student version of TopSpin for $90 for a
3-year license. I will be recommending this to our users who want their
own off-line processing.
In my limited experience importing array'ed VNMR data, TopSpin converts
it to a 2D dataset, without any problems. Of course if you wanted
separate TopSpin data sets for each array element you could extract
traces from the 2D and resave them, a bit of a chore if there are a lot
of traces! Although there might be a macro or au program already
written to do this.
I am generally very impressed with TopSpin. I'm sure you could get a
demo license to try it yourself. We are running TopSpin offline under
Red Hat 5. If you do this you need to have the KDE desktop installed.
In my experience TopSpin would hang quite a bit if I tried to run it
using Gnome with RH5.
2************************************
vconv works in topspin just like it does in xwin, except there is a gui
now. I *think* the only real difference between xwin and topspin was
the gui,,, and now 4 or 5 years of new hardware and development. It
works ok, but spectra from VXR-S instruments seem to be a little noisier
than vnmr 6.1c would have you believe.
3************************************
I use Topspin 2.1 fairly often to work on data from our instruments
using Vnmr6.1C. Works very well in my opinion. Sometimes you have to
test out different parameters for processing in order to get them right
(for example, selecting TPPI vs. States for a 2D transform) but overall
I like it.
Bruker just announced a student version of Topspin for 99 Euros. Our
Bruker sales person says it can import Varian data. The only things
missing are acquisition related modules.
4************************************
Yes, I do this every now and then. In Topspin under the File tab, click
Open. It will ask what format, choose Varian. You have to set up the
data so it fits Topspin format. Filename from varian becomes the name,
designate an expno and procno (usually 1 for each). The processed data
gets written to a directory (dir) and a user. Topspin looks for data in
Bruker format, which usually is /opt/topspin/data/directoryforuser/nmr
---the Linux format or C:/Bruker/Topspin/data/directoryforuser/nmr ---
format for Windows PCs. The data can then be processed with Bruker
commands. Check formats -- for 1D use standard line broadening, then ef,
apk, abs, xwp to set up graphics files (the plotter format is given
under the PROCPAR tab--close to the bottom of that page. I use +/1H+pp
(a standard 1D with peak picking). 2D data sets are a little trickier
to process. Topspin doesn't immediately recognize if the data is
States, States/TPPI, echo/antiecho.... The fastest way is to try the
transform until the data looks right. Again you change this in the
PROCPAR tab about half way down this page. Again the plotter format
needs to be set so you can print it out. My copy of Topspin1.3 doesn't
get the indirect nuclei chemical shift correct, unless its 1H. If you
need more or specifics, I can walk you through.
5************************************
In TopSpin go to:
File -> Open ->
In the windows "Option" choose Open NMR data stored in special formats
and in the field "required parameter", select File type = VNMR and click OK
Then browse for the file and click on "VNMR Data Conversion"
6************************************
Many of the students here use Topspin on their laptops, and I've heard
that they like it because they can process both B & V data.
7***********************************
Yes it works quite well. Just choose File ŕ open, “Open NMR data stored
in special formats” ŕ select VNMR. Click ok, browse for the FID folder
and give Topspin the proper name, experiment number, and directory
(C:\Bruker\TOPSPIN) to put the data once converted.
1D are very straight forward, 2D and 3D take a little finesse to get the
processing parameters set properly. Remember the State-TPPI, STATES,
and TPPI have different definitions between Bruker and Varian. However
once set correctly it works great.
We are actually setting up a server to process all data collected with
Topspin. I’ll have a better idea of how straight forward this is for
the standard user that collects with VNMRJ and then attempts to process
with Topspin in the coming months.
8***********************************
Try ``vconv'', worked fine for me.
9***********************************
Generally speaking, the software of each NMR vendor can import data
formatted on another vendor's machine. This is the case with TopSpin. Of
more importance than importing is whether the original data format is
maintained. In the case of TopSpin, the data is converted to the
standard Bruker data format. Then, it's just like the data for which the
software was written.
10***********************************
Topspin imports Varian data quite well. With 2D you have to adjust the
parameter MC2 that defines the acquisition mode in the indirect
dimension. Most other parameters are being imported.
11***********************************
It works fine. Before we retired our Varian, I routinely imported the
data into Topspin to process it, because I have TS on my desktop pc and
didn't have to sit at the spectrometer.
It works like it did in XWIN.
12************************************
It works... I have Topspin on my notebook computer, and on my new 300.
I was "Playing" with Topspin before my instrument arrived using Varian
data. It's a little flaky, though, for some 2D datasets.
As you might recall, I purchased a University-wide site-license for
MestreNova, and all of my users are expected to use MNova for their
Varian and Bruker data. Therefore, I don't intend for my users to use
Topspin for data processing, even for the Bruker data.
13************************************
Topspin is compatible with Varian data. We actually have a Topspin
offline data processing computer for both Bruker and Varian NMR data.
14************************************
Yes, it does. It is quite straightforward too. It usually need to
re-reference the spectra after import.
15************************************
Another approach might be to ask the folks with the Varian instrument to
export the data into any fairly recent Bruker format. In addition,
Third Party software vendors (eg. Mestrelabs) are, of necessity, good at
digesting data from a variety of sources.
16************************************
It works quite well in my experience. Us the TopSpin menu and import
Varian data and it should work ok. We haven't tried it for all types of
spectra but so far, so good.
17************************************
This is fairly easy. From the File drop down menu select Open and then
the option "Open NMR data stored in special formats" and, from the file
type drop down, select VNMR.
18************************************
From Mike Engelhardt:
TopSpin2 will convert all types of 1D, 2D and 3D VNMR datasets. I have
not been notified lately with any difficulties or new dataset formats
that would not work. If anybody comes across such a dataset, please send
it to us at nmr-software-support_at_bruker.de and we'll check it out.
AND Mike's separately posted to the AMMRL group on July 14, 2009:
Dear NMR users,
as far as I know, a mail has already informed you about the 'vconv'
command in TopSpin. To the best of my knowledge, (almost) all VNMR
datasets are handled correctly by 'vconv'. One thing that's a bit hard
for us to find out is the correct "MC2" flag for the Bruker processing.
You can create a parameter set with the name of the VNMR pulse program
and set "MC2" in it. If such a parameter set exists, it will be used as
the base parameter set for the converted dataset and MC2 is correct from
the start.
If you encounter problems with the conversion, you can always send this
VNMR dataset to nmr-software-support_at_bruker.de and we'll have a look.
Best wishes, Mike !
19************************************
Yes, TOPSPIN 2.5 can import Varian data sets with the command vconv, and
provided that you stipulate the correct path for the converted data set,
it will allow processing as usual, as if it were native Bruker (well,
almost). That works smoothly with the 1-D data sets.
However, opening the plot function in TOPSPIN does throw up a few
complaints, which after cancelling repeatedly, eventually does give the
usual functions of the plot window.
By the way, I should add that we are running TOPSPIN 2.5 in WIndows in
SUN's Virtualbox on an iMac. We can import the array data sets as well,
but sometimes lose some of the stragglers towards the end of the array,
though not sure why as yet. Also some 2-D data sets recently would not
convert, again not clear why, because re-runs of the same experiment
were fine.
We have also performed the same process on PC's running TOPsPIN2.5,
with similar behavior.
We used to perform the same operation with xwinnmr, but haven't tried
topspin1.3 etc.
20************************************
I use Topspin 1.3 & now 2.1 to routinely process Varian 1D & 2D on my PC
(since Varian are still struggling to port VJ to Windows, apparently).
The conversion process is very straight forward & I have made a short
Powerpoint to provide to our cross-platform users who do off-line
processing on Windows machines (& have forked out the $$$s for a Topspin
licence).
21************************************
There is no problem to import VARIAN data into TOPSPIN. The only problem
might be to enter the correct path into the command line since the
manual is not quite easy-reading. If you or your postdocs need further
assistance, please let me know.
22************************************
I am using Topspin version 2.1 running on a PC under windows XP.
As regards import of Varian 1D data (VNMR 6.1C on solaris), this appears
to work well for us.
We FTP the data over to the Bruker PC. The conversion command is vconv
which we have incorporated in to a Topspin 'button'. A dialogue ensues
where you browse to the varian file to be converted, a new dialogue
window comes up where you can select the directory the Bruker form
should be stored in and an available expno. Have less experience with 2D
conversions.
23************************************
I have used the "vconv" function in TopSpin (v1.3) occasionally. I have
never had a failure with importing (admittedly) fairly basic 1D and 2D
homonuclear data. Id be happy to test out some data conversions for you
if you want to zip up some files and send them on as a test.
24************************************
I have imported Varian data to TopSpin. My TopSpin data is stored on my
D:-drive in D:\TopSpin data\data\flname\nmr
In TopSpin:
File / Open / Open NMR data stored in special formats
File type = VNMR
In VCONV window:
VNMR-name = (full path to the Varian fid file)
Name = filename (without the .fid extension)
Expo = 1
Dir = (directory name of location of TopSpin data on your system. On
my system it is D:\TopSpin data)
USER = (user filename for TopSpin data. On my system it is flname)
Note: The parameters appear to copy over into the new file, but I can
not directly open the spectrum print into a print layout. My current
work-around is to open some other Bruker-generated spectrum into the
desired Print Layout, delete the parameter listing, and then use Edit to
switch the Data Set to the desired converted Varian spectrum.
Not perfect, but it gives me the spectrum.
25************************************
I know several students here do prefer to work up their Varian data in
TopSpin. We have Topspin 1.3, and to open the data, you go to File,
Open, and then select Open NMR data stored in special formats. Select
VNMR from the File Type drop down menu, pick the file you want to open,
and then click VNMR data conversion. Fill in the information for the
data location, and you are all set.
As far as I know, this works well. There is also a command (vconv) that
you can type in the TopSpin command line that does the same thing. I've
never actually tried this method, but I assume it works the same way.
Received on Tue Jul 14 2009 - 07:14:20 MST