Hi Martin,
Welcome to the relax mailing lists! I'll try to answer your
questions, but the second point might require a little bit of work:
1). Single-scan interleaving will keep the temperature constant
through the experiment. And the MeOH calibration should be reasonable
for relatively low-powered experiments and where small temperature
changes are not important. However the standard MeOH calibration of a
spectrometer is useless when you are running experiments which pump in
large amounts of power into the probe head.
But it needs to be noted, that an R2 CPMG experiment has very
different heating properties to an R1 experiment. The R1 should be
about the same temperature as a HSQC and be close to the standard
MeOH/ethylene glycol sepectrometer calibration (though this needs to
be checked and calibrated using MeOH for lower and ethylene glycol for
higher temperatures). The R2 and, to a lesser extent, the NOE
pre-saturation add a lot more power into the probe head. The CPMG is
punishing, its not too difficult to fry a probe head. The differences
can either cause the temperature in your sample to be too high or too
low. This is unpredictable as the thermometer used by the VT unit is
next to the coils in the probe head and not inside your sample. So
the VT unit tries to set the temperature of inside of the probe head.
However your sample is not where the thermometer is - in between it
and the thermometer is the water of the sample, the glass of the tube,
the air gap where the VT unit controls air flow, and the outside bits
of the probe head protecting the electronics. If you change the
sample, the probe head, the VT unit, or even the magnet, this will
have a different affect on temperature. The VT unit responds
differently under different conditions and sometimes over or under
compensates. For example when running the R2 experiment at 25 degrees
I have seen that on the Varian 500 I was using, the actual sample
temperature was ~23 degrees whereas on the 600 the temperature was
close to 27 degrees (or maybe it was the other way around, I don't
remember exactly). This type of temperature variation is fatal for
any type of relaxation data analysis. Maybe on your spectrometers the
variation is not so great. But you will still need to check.
This issue has been discussed a number of times before. For example
see the threads at:
https://mail.gna.org/public/relax-users/2011-07/msg00008.html
https://mail.gna.org/public/relax-users/2011-07/msg00011.html
https://mail.gna.org/public/relax-users/2007-06/msg00001.html
https://mail.gna.org/public/relax-users/2008-05/msg00008.html
I think you'll find some interesting info about temperature
inconsistencies and what happens when that is the case in these posts.
2). For this point, I'll send another email. This is to start a
separate thread for the Mac OS X problem.
Cheers,
Edward
On 23 March 2012 11:09, Martin Ballaschk <ballaschk@xxxxxxxxxxxxx> wrote:
Dear relax-users,
I am just beginning to record and analyze relaxation data for MF analysis.
So far we collected data at 600 MHz, and a second data set at 750MHz is
planned.
I have two questions I hope you can help me with:
1) Temperature calibration
We use single-scan interleaving to account for a constant temperature
during the whole experimental series. We also use methanol to calibrate the
spectrometer's temperature sensors. As we found out, every magnet is
different and the on-screen parameters cannot be trusted. We have tables
where This procedure is not done with the T2 measurements in mind, however.
Isn't it also important that R1 and R2 measurements have the same
temperature – how do you check for that?
How can I check differences in sample heating between different magnets due
to different air-flow etc? How to compensate for these temperature
differences? Do I need different pulse programs that account for
temperature differences for every spectrometer? Or is the difference
insignificant once the spectrometers have been calibrated?
2)
In Mac OS X ("Lion", 10.7.3), the self-contained relax Application bundle
is crashing and is giving just an "relax error" and the option to
"terminate" or "open the Console".
I can run the “relax” script which is sitting inside
relax.app/Contents/Resources/ and I get a prompt, but only after installing
numpy via Macports. If I don't, relax complains that numpy is not installed.
After installing wxPython 2.9 via the official installer "./relax" -g is
attempting to start (I can see the splash screen), but then halts with the
errors.
Interestingly, I found out today that it seems to run just fine if I run
the relax binary in Contents/MacOS by dropping it onto Terminal.app!
(I did not test this without numpy and wXPython seperately installed.)
What's your experience? What do you think is broken – my system (10.7) or
something inside the application bundle?
Cheers
Martin
***
RELAX ERROR MESSAGES FROM THE CONSOLE
15.03.12 15:19:15,538 relax: relax Error
15.03.12 15:19:17,667 com.apple.launchd.peruser.501:
([0x0-0x14e14e].com.nmr-relax.relax[70595]) Exited with code: 255
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax: <_FuncPtr object
at
0x101b0dc80>
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax: Traceback (most
recent call last):
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax: File
"/Applications/relax.app/Contents/Resources/__boot__.py", line 179, in
<module>
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax:
_argv_emulation()
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax: File
"/Applications/relax.app/Contents/Resources/__boot__.py", line 177, in
_argv_emulation
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax:
_get_argvemulator().mainloop()
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax: File
"/Applications/relax.app/Contents/Resources/__boot__.py", line 101, in
mainloop
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax: stoptime =
Evt.TickCount() + timeout
15.03.12 15:19:22,227 [0x0-0x14f14f].com.nmr-relax.relax: AttributeError:
'module' object has no attribute 'TickCount'
--
Martin Ballaschk
AG Schmieder
Leibniz-Institut für Molekulare Pharmakologie
Robert-Rössle-Str. 10
13125 Berlin
ballaschk@xxxxxxxxxxxxx
Tel.: +49-30-94793-234/315
Büro: A 1.26
Labor: C 1.10
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Re: Temperature calibration & relax @ Mac OS X 10.7. 3 „Lion“