[3dem] MicroED on small molecule

Mon Jan 19 02:22:45 PST 2026

using optical tweezers to manipulate micro crystals?

On Mon, Jan 19, 2026 at 10:49 AM Guillaume Gaullier via 3dem <
3dem at ncmir.ucsd.edu> wrote:

> Hello,
>
>
> I have never done microED, and from your pictures it looks like the
> crystals are already well separated (except for the smaller ones growing at
> one end of larger ones), so take this suggestion for what it's worth...
>
>
> When weighing powders of small molecules that tend to stick to tubes and
> spatulas by static, one can zap tools and powder with an "anti static gun"
> to cancel out charges, and this often greatly alleviates such problems. See
> here: https://urldefense.com/v3/__https://www.fishersci.com/shop/products/anti-static-gun-2/nc9663078__;!!Mih3wA!HFSHkOlJkVUCfQRYUxXN_rnSJgqnT739MVWfbnNYi_TZPUmgqi_gYK9z2Pe7U8dccJ8_SctwtZHGII4PU9zJZxE$ 
> <https://urldefense.com/v3/__https://www.fishersci.com/shop/products/anti-static-gun-2/nc9663078__;!!Mih3wA!CDXA2I2x2rPE9lGHYeJBN2R7Zt6HeDVAQEQKIKxXkQcGlXGr6HAZ6ipjF9wazHf4dIP-opUbrpliRDT8JnyR4zm1AhfrQFyw$>
>
> I have also seen this kind of anti static device built directly into some
> fine scales (the kind sensitive enough to measure mg amounts accurately).
>
> Such treatment might also help separating crystals better?
>
>
> Cheers,
>
>
> Guillaume
> ------------------------------
> *From:* 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Takanori Nakane
> via 3dem <3dem at ncmir.ucsd.edu>
> *Sent:* Monday, January 19, 2026 10:21:01 AM
> *To:* Yu, Xiaodi [JRDUS] via 3dem; Yu, Xiaodi [JRDUS]
> *Cc:* 3dem at ncmir.ucsd.edu
> *Subject:* Re: [3dem] MicroED on small molecule
>
> Hi,
>
> Looking at your crystals, I feel the crystal density is OK.
> Certainly several smaller crystals are attached at the bottom
> of the main plate. However, they are much smaller than the main
> plate and their orientation is different. Thus, I guess the dirty
> spot shape is caused by the property of the main, plate-shaped
> crystal itself. Indeed, it has wrinkles on it.
>
> Regarding data processing:
>
> DIALS can index multiple-lattice and (optionally) remove overlapped
> spots but cannot deconvolute overlapped intensities.
> I myself process the dominant lattice alone.
> Because I collect 100 - 500 crystals and work at a very high
> multiplicity (usually 50 - 300), I can select better crystals
> with less overlaps. Even if some reflections are overlapped,
> their intensities are averaged out and/or rejected during
> scaling and merging.
>
> I agree that ideally multiple lattices should be avoided.
> But whether this is practically possible and worthwhile
> depends on the goal of the experiment and the availability
> of the scope time.
>
> In our case, the goal of most experiments is the understanding
> of packing and conformations. We don't pursue very high
> accuracy in molecular geometry. Moreover, other sources
> of systematic errors (multiple scattering, lens hysterisis,
> inaccurate camera length) probably have bigger influences
> on the final model accuracy.
>
> Another issue is that we have only one weekend beam time in three to
> four weeks. In one session, we can load up to 9 grids of
> various compounds (bottom three slots of a cartridge tend to
> get frosted) in one go, only once. Thus, we cannot try-and-error
> various pre-treatments, optimizing solvents and sonication duration.
> In my experience, even when a chemist says a solvent (say, hexane)
> is a poor solvent and does not dissolve a compound, the crystal
> often melts a bit on the surface and diffraction becomes worse.
> Sonication and grinding also damages crystals often.
> This depends on the crystal; some crystals are
> hard and very robust. We need to test and optimize various parameters.
> But we cannot afford that, unless absolutely necessary.
>
> TFS scopes with an autoloader are great for automatic data collection
> over night or over weekend but not convenient for successive grid
> exchanges, as all grids have to be pulled out simultaneously.
> JEOL scopes are better in this regard, as they allow swapping
> only a subset of the loaded grids.
>
> Best regards,
>
> Takanori Nakane
>
> ________________________________________
> From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Yu, Xiaodi [JRDUS]
> via 3dem <3dem at ncmir.ucsd.edu>
> Sent: 16 January 2026 23:39
> To: Tim Gruene; Yu, Xiaodi [JRDUS] via 3dem
> Subject: Re: [3dem] MicroED on small molecule
>
> Thanks everyone — these are very helpful suggestions: recrystallization,
> resuspending the sample in solution (with or without sonication),
> sliding glass plates, and more. We’ll try each approach. I hope this
> thread helps not just our research but others facing the same trouble.
> I’ve uploaded a couple of images showing the issue; we’re using a
> Glacios without SA.
>
> Best,
>
> Xiaodi
>
> ________________________________________
> From: Tim Gruene
> Sent: Friday, January 16, 2026 4:32 AM
> To: Yu, Xiaodi [JRDUS] via 3dem
> Cc: Yu, Xiaodi [JRDUS]
> Subject: [EXTERNAL]  Re: [3dem] MicroED on small molecule
>
> On Thu, 15 Jan 2026 18:37:05 +0000
> "Yu, Xiaodi \[JRDUS\] via 3dem" <3dem at ncmir.ucsd.edu> wrote:
>
> > Hi everyone,
> >
> > I’d like to consult MicroED experts about a small‑molecule sample:
> > the powder contains diffracting microcrystals, but they stick
> > together and make data collection difficult. Does anyone have
> > recommended approaches or tips to prevent clumping and improve data
> > collection?
> >
> > Thanks in advance,
> > Xiaodi
> >
>
> Dear Xiaodi,
>
> my experience is slightly different from Takanori's. We put a lot of
> effort in sample preparation, so as to get as good data as possible
> rather than leaving it to the software to deconvolute multiple
> lattices. No matter how good the software (even talking SAINT/TWINABS
> ;-), a dataset from multiple lattices is hardly ever as good as a single
> crystal dataset.
>
> Our goal is a sufficiently dilute crystal density on the grid so to
> have isolated particles. Like Takanori, match the beam diameter to the
> crystal size. For organic and metalorganic samples, this can be 2-3um
> in diameter. Smaller diameter is a greater challenge for how good you
> can centre the crystal and the stability of the rotation axis.
>
> My personal favourite is a suspension, because it is reproducible. The
> liquid must match two requirements:
> - it evaporates
> - it does not modify the crystal structure
>
> In suspension, we either vortex the sample, or place it in a sonication
> bath. This can be up to several minutes, depending on how strongly they
> stick. The lab record for a zeolite was about 1-2 hourse.
>
> n-hexane is a good candidate to start, but also isopropanol, MeOH,
> EtOH. You can check water, too.
>
> Sometimes particles stick together while you watch the solvent
> evaporate. To reduce their time of socialization, you can either dip
> the grid vertically to the suspension surface.
>
> Or you add a drop to the grid and suck off the supernatant from
> underneath: lacey carbon makes a great sieve for crystals.
>
> By creating a dilution series, we typically get to the ideal density
> with 3-5 trials.
>
> Good luck!
>
> Tim
>
> P.S.: in Europe, there is a great number of installation of electron
> diffractometers (more than a dozen at least), and the Bruker mailing
> list or the CCP4bb may also be great resources for crystallographic
> questions. Crystallography is not an imaging techniques, while
> TEM is.
>
> --
> --
> Tim Gruene
> Head of the Core Facility Crystal Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
>
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