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 <[email protected]> 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 > [email protected] > Tel.: +49-30-94793-234/315 > Büro: A 1.26 > Labor: C 1.10 > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-users _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
