Dear Bruker Users'
I wish you all a Healthy and Happy New Year !
Thank you, Markus, for providing an "answer" mail to your original
enquiry :-)
And I would like to add one comment to Markus' mail. I stated:
"Option 1:
you need to make a physical copy of the used vdlist to the EXPNO
directory.
There's no need to manipulate the acqu(s) files, it's enough to just
copy
the file vdlist under that same name to the EXPNO directory."
With this I mean: whatever list you use for the simulation, it's enough
to copy it to the EXPNO directory afterwards. All you need to do is give
it the name "vdlist" and select this name in the T1/T2 relaxation
parameters as the list type. This should avoid the manipulation of the
acqu(s) files.
Best wishes, Mike !
===================================================================
... ... Dr. Michael Engelhardt
. * . . Service and Support Manager
. . . . Bruker BioSpin GmbH
B R U K E R Silberstreifen
. . . . D-76287 Rheinstetten
. * . . Voice: +49-721-5161-440
... ... Fax: +49-721-5161-943
Email: michael.engelhardt@bruker.de
===================================================================
-----Original Message-----
From: by way of BUM <bruker-users-mail@purcell.cchem.berkeley.edu>
[mailto:mhoffman@brockport.edu]
Sent: Wednesday, January 03, 2007 9:46 PM
To: BUM
Subject: Some answers regarding NMR simulator questions
Hi everyone,
I am typing some answers right into text of my previously stated
questions
about NMR simulator.
My thanks goes to Pavel Kessler, Michael Engelhard and Amy Freund for
providing me with helpful feedback.
Another generic comment I'd like to pass on regarding NMR simulator is
as
follows. If you are considering acquiring the teaching licenses that
contain NMR simulator beware that these clash with any existing
processing
licenses (that don't come with NMR simulator). Two servers would need
to
be set up. I ran into this issue and in the end I still don't know how I
would set up two servers. Instead, the problem was solved by forgoing
the
teaching licenses and exchanging them with NMR simulator-only licenses,
where we just simply had to add the license code text to the license.dat
file for our existing processing licenses.
All the best,
Markus
Dear Bruker Users,
For teaching purposes, I have been in the process of learning how to use
NMR
simulator. (We use Topspin 1.3.) I ran into two main issues I have not
been
able to resolve on my own. Any hints to point me in the right direction
are most welcome.
1.) I am unable to successfully simulate a selective presaturation
experiment. I did make sure that the simulation is set to full
relaxation,
the spin system has values for T1 and the offset is properly set. I
suspect
it has to do with setting the powerlevels. NMR simulator uses absolute
values in Hz units and I just have no good handle in assessing what
values
are appropriate, even after reading the little bit of info available in
the
NMR simulator manual on page 108. I tried by trial and error a number of
settings but to no avail.
The current NMR-Sim version does not simulate relaxation
during rf pulses ( see Chapter 2.2 Relaxation) and so you cannot
correctly simulate sequences using a long cw pulse for presaturation.
2.) I was successful in simulating a T1 experiment. It would be nice to
have
students use the same relaxation analysis in Topsin 1.3 to confirm the
known T1 value. However, the delay list information does not transfer
over
from NMR simulator to the obtained data set visible in Topspin, and the
relaxation analysis module does not work. I re-created the delay list,
but
this still does not seem to get recognized by the relaxation analysis
routine.
This problem will be fixed in next patch level. As for now there are two
options around it by modifying the data files outside of Topspin. I was
able to work out option 2:
Option 1:
you need to make a physical copy of the used vdlist to the EXPNO
directory.
There's no need to manipulate the acqu(s) files, it's enough to just
copy
the file vdlist under that same name to the EXPNO directory.
Option 2:
Once the data is generated by NMRSim, and transferred to Topspin, you
will
need to
(a) manually add the delay list to the experiment's directory, not the
general Topspin directory for vdlists. Go to <Topspin home>/data/<user
name>/nmr/<experiment name>/<EXPNO> and edit the acqu and acqu files
name>with
the name of the delay list. You can easily edit the acqu directory
within
Topspin instead of editing the text of the file, but the status file,
acqus
will need to be edited outside of Topspin.
(b) add the actual delay list file to the same directory listed above.
Be
sure there is no .txt or other extension in the file name.
Markus Hoffmann
Department of Chemistry
SUNY Brockport
Phone: (585) 395-5587
FAX: (585) 395-5805
mhoffman@brockport.edu
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