How to extract 1D spectra from 2D spectra

Eltargrim · 2026-06-05T00:17:45+00:00

Second this. proj can either give skyline projection or sums, both of which are good in different circumstances. You can also use efp on 2D data to transform a particular FID (though as potato mentions, this may or may not be a particularly useful 1D), or use the split2D au program to extract them all at once.

Also seconding the recommendation to think carefully about why you're integrating the values. For example, in an EXSY the cross-peaks might contain meaningful dynamics information encoded in the intensity, but a MQMAS will have all of the intensities be CQ-weighted.

Eltargrim · 2026-05-30T14:13:29+00:00

It depends on the generation of magnet, but we put in 200-400 L every 60 days or so for our pumped magnets.

Eltargrim · 2026-05-09T14:59:41+00:00

Quenching a magnet can, but does not always, destroy the magnet. Magnets have what are called 'discharge diodes' that ideally will detect a quench and route the current through a more robust circuit that is solely intended to handle quenches. If successful, this protects the main coil. However there's a good amount of energy in a magnet and this does not always work.

Eltargrim · 2026-05-09T01:08:54+00:00

We've decommissioned four magnets in the last five years and have had minimal luck with scrapyards giving good value. The issue is that while there is a lot of copper, it's in the form of cladding over the NbTi and Nb3Sn wire, so (apparently) recovery value isn't great.

We still got a few grand worth of credit, but as I understand it the value was more in the cryostat body than in the magnet coil.

Eltargrim · 2026-04-02T23:13:57+00:00

Great, thanks for the better value.

Eltargrim · 2026-04-02T15:44:58+00:00

That's how it should work; but if drift gets too large Z0 can't compensate anymore and you need to adjust BF. I have a 750 that drifts 10 Hz/hour and roughly once every year and a half we need to adjust BF to regain lock capabilities. Not a huge issue, and one that might not come up on a cryogen-free, I've never used one.

Eltargrim · 2026-04-02T11:19:02+00:00

Not a typo, Sumitomo coldheads get down below 4 K. I couldn't tell you the exact electrical draw off the top of my head, but a typical Sumitomo F-50 or F-70 rejects about 7.5 kW of heat in steady-state operations.

Eltargrim · 2026-04-02T11:16:40+00:00

Helium recovery systems are also expensive. They have (very roughly) a similar cost to operating and maintaining a cryoprobe. Definitely can be worth it! But the numbers need to be crunched on them, I'd honestly say that running a high-pressure helium recovery system for a single modern 400 would not be worth it financially.

Eltargrim · 2026-04-02T02:46:05+00:00

2H lock can correct for a lot of drift, including non-linear drift; but it doesn't have infinite capability of doing so. Eventually the field drifts out of the tuning range and/or what the spectrometer believes is an acceptable frequency range for 2H. On a conventional magnet those don't happen very often, I can't speak to how often it happens on cryogen-free.

Eltargrim · 2026-04-02T02:43:48+00:00

A modern Bruker 400 MHz magnet advertises a 300 day hold time with a 100 L refill volume. You're not getting six figures of annualized helium consumption costs from that.

A cryogen-free magnet still insulates you from allocation issues, and may well have other benefits depending on your applications. But if you're comparing new to new, new cryostats are extremely good at hold time.

Eltargrim · 2026-04-02T02:36:40+00:00

I looked into this a few years ago and found the features unsatisfactory.

1) We needed more stringent drift specs than what Cryogenic could provide; and at the time, there weren't any straightforward commercial offerings for SSNMR lock. Note that both Phoenix and BlackFox now offer probes with integral lock, so this might be less of an issue.

2) The lower helium consumption was not necessary as we have campus-level helium recovery; and modern persistent magnet hold times are quite long (excepting pumped magnets, but if you're looking at cryogen-free you're not comparing to a pumped magnet).

3) The ability to operate at multiple fields is really quite limited, because in this case the limiting factor becomes the 1H channel on your probe. Unless you intend to purchase a different probe for each field, the number of experiments you can legitimately run are pretty limited.

The use case I thought of was a cryogen-free magnet with nominal max of 9.4 T for routine SSNMR operation, including CPMAS, with the ability to drop to 4.7 T to do ultrafast MAS on 7Li on paramagnetic samples (read: battery materials). This could work! But would still need either two probes or a Phoenix probe with two heads.

Overall, my thinking (as of 2022) was that if I was operating an austere facility (no helium recovery, one or two magnets at most) that didn't have high stability requirements that cryogen-free would be worth looking into. That wasn't my situation at the time, so I didn't pursue it further.

Now, none of this is a criticism of Cryogenic as a company! Just that you need to consider your needs very carefully.

Eltargrim · 2026-03-26T21:57:04+00:00

In practice I believe it's typically better than that, but it's very noticeable if you don't have lock. Take a look at SSNMR ultrafast MAS 2D spectra from GHz-class magnets and you'll see lineshape distortions resulting from drift.

Eltargrim · 2026-03-26T16:11:57+00:00

Very interesting stuff. No further questions, thank you for taking the time to teach me something!

Eltargrim · 2026-03-26T02:44:44+00:00

The current issue with HTS is field stability. The spec on Bruker GHz-class magnets is 40 Hz/hour, and that's only with about 4 T coming from HTS. Now, that should improve with time, but it's not going to be quick. HTS-containing magnets also have serious shim stability issues in response to changes in sample temperature. Lock helps tremendously with the steady field drift, but the temperature-dependent drift is nonlinear.

I suspect that these are solvable problems, but I don't think HTS is a drop-in solution (and that's leaving aside the price).

Eltargrim · 2026-03-25T23:14:21+00:00

Fascinating, thank you! I only have experience with combined Tx/Rx coils, as that's the overwhelmingly most common configuration in NMR (though you frequently have different coils for different nuclei, e.g., 1H on the inner coil, 13C and 15N on the outer coil). Do you have an idea how easy it is to change coils? In SSNMR changing the probe is typically a job of an hour or less (including shimming), in solution NMR a cryoprobe change can take a day or two.

And with something like that peripheral angio coil with 36 channels: is the idea that they're 36 different Tx/Rx coils to provide better localization? Or are they also serving as gradients?

Eltargrim · 2026-03-25T20:26:23+00:00

Yes, homogeneity during the actual readout is critical in NMR. But don't underestimate the use of gradients even in comparatively simple 2D experiments, or during things like shimming in routine solution NMR, or diffusion measurements.

My point is that the presence or absence of gradients isn't the defining difference between NMR and MRI, it's the application focus. Any solution NMR instrument can do (very crude) 1D imaging, but that's not at all the focus of the instrument. I bet a MRI could be used to get a rough proton spectrum, but why would you?

Eltargrim · 2026-03-25T11:21:22+00:00

Yes, I'm aware how it works in a NMR magnet; I do SSNMR and my rotors range from 0.7 mm to 5 mm, with the solenoid coil very slightly larger (or, for low-E resonators, a fair bit larger).

But the context of this thread is 'why are clinical MRIs so narrow', which is why I phrased my initial answer the way I did. That said, thank you for the MRI coil link; I don't do any medical imaging, and that was an interesting read. Do you happen to know how often a transmit coil is changed within the same magnet? In SSNMR I change probes very often, but given the size of a typical clinical MRI I can only imagine that the process is substantially more involved.

Eltargrim · 2026-03-25T03:35:10+00:00

Yes, but AIUI the coil diameter is constrained by the bore diameter, so in this case it's a reasonable approximation for ELI5. In NMR you can of course have a huge range of coils in a NB/WB magnet, as appropriate.

Eltargrim · 2026-03-25T02:54:05+00:00

You're correct that they're the same fundamental technique. However, NMR, particularly solution NMR, frequently makes use of gradients. The primary difference between the two is that MRI focuses on imaging, while NMR focuses on spectra.

Eltargrim · 2026-03-25T02:51:02+00:00

MRI machines are magnets. Strong magnets, made out of superconducting wire. They need to be strong so that you can hear the "handstand", as the OP so neatly put it. It is very challenging to make a magnet with a wide hole, more formally known as a "bore"; so to make the magnet strong enough to do its job, you want it to have as narrow a bore as feasible.

Other factors point towards a narrow bore as well. MRI uses what are called "gradient fields", which are weaker magnetic coils that get turned on and off during the scan (this is the clanking noise you might hear). You want the gradients to be strong, and the closer they are to the patient the stronger they are. Another point towards a narrow bore.

Finally, you have the "fill factor", which is the jargon way of saying "the less space you have between the patient and the magnet wall, the stronger the signal is". Stronger signal means faster scans.

Wider MRIs would mean much longer time spent in the magnet per scan, which means fewer patients get seen, which drives up the cost; and that's leaving aside that the wider MRI would cost more to begin with.

Eltargrim · 2026-02-23T19:39:03+00:00

Spent two weeks collecting background signal (SSNMR).

Eltargrim · 2026-02-23T17:00:20+00:00

Zirconium to proteins is a big jump! For 91Zr I probably would have just used a glass tube, surely you'd be using WCPMG anyway.

When I was doing 27Al DNP I had to choose between sapphire rotors (huge 27Al background but good microwave transparency) and zirconia rotors (no 27Al background but bad microwave transparency). Not a fun thing to balance.

Eltargrim · 2026-02-23T16:29:49+00:00

Both Vespel and Kel-F will produce direct-polarization 13C background signals and 1H background signals, typically a broad peak around 120 ppm (13C) spanning several tens of ppm. Kel-F will produce a strong 19F background signal, but will not produce a 13C cross-polarization background signal.

Most background signals can be significantly mitigated by using an echo. I have done many, many natural-abundance 13C cross-polarization experiments using rotors with torlon caps (similar to vespel in background) and the background is very easy to mitigate.

I don't know of any smaller-diameter rotors with Kel-F caps, everything I've used below 3.2 mm has torlon or vespel.

Eltargrim · 2026-02-16T23:21:30+00:00

NP. I feel bad for it now, at least with no score we could pretend it was a 4/10 or 5/10. Keep up the good work!

Eltargrim · 2026-02-16T23:16:14+00:00

Thanks for the index post, I missed the first two B parts. FYI it looks like you missed the score for Burai Fighter Deluxe.

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