[3dem] MicroED on small molecule (William J Nicolas)
William Nicolas
william.nicolas.pro at gmail.com
Mon Jan 19 17:32:00 PST 2026
Hello,
Just my 2 cents about how to improve size of crystals for microED:
*
Sonication can break up crystals.
*
Solubilization of powder with solvent such as acetonitrile or acetone, laying a drop on the grid and letting solvent evaporate on the grid in vacuum will trigger recrystallization. Depending on project this can help.
*
FIB-milling of course but this defeats the purpose of high throughput.
I recommend looking into the small molecule papers from the Gonen lab and also this protocol that describes these procedures: https://urldefense.com/v3/__https://www.nature.com/articles/s41596-024-01088-7__;!!Mih3wA!A-2dWoa3-KbaN9SdwFy8hsDb6oFAmlZT_0_YGhmooJGc-mLmVfoPCNLilLrnujyrhw2jUkVL9jPiDsqcR3VMEUP-sE7_tw$
Hope this helps,
William J Nicolas - PhD
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of 3dem-request at ncmir.ucsd.edu <3dem-request at ncmir.ucsd.edu>
Date: Monday, January 19, 2026 at 3:06 AM
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Today's Topics:
1. Re: MicroED on small molecule (Guillaume Gaullier)
2. Re: MicroED on small molecule (Jaime Llodra)
3. Postdoc position at MRC-LMB, Cambridge UK (Suyang Zhang)
----------------------------------------------------------------------
Message: 1
Date: Mon, 19 Jan 2026 09:48:56 +0000
From: Guillaume Gaullier <guillaume.gaullier at kemi.uu.se>
To: "Yu, Xiaodi [JRDUS]" <XYu6 at its.jnj.com>, "3dem at ncmir.ucsd.edu"
<3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] MicroED on small molecule
Message-ID: <76aeed52a47b418e8e02bd3548fadf90 at kemi.uu.se>
Content-Type: text/plain; charset="utf-8"
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!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
https://urldefense.com/v3/__https://ccsa.univie.ac.at__;!!Mih3wA!HD3edpvrNnrwqJcjr0poHrj-8C7Vz9d26HDyYgX2ofMcuF0eliP_uLCj50AyQWhK91-uVk1ThTy0qqs2$
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Message: 2
Date: Mon, 19 Jan 2026 11:22:45 +0100
From: Jaime Llodra <jaimellodra at gmail.com>
To: Guillaume Gaullier <guillaume.gaullier at kemi.uu.se>
Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] MicroED on small molecule
Message-ID:
<CAPnh1Ac5EWqygPELW1Xh=7+ROxZdm6pWqnTQGwJ4E2j4=n=npA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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
>
>
> https://urldefense.com/v3/__https://ccsa.univie.ac.at__;!!Mih3wA!HD3edpvrNnrwqJcjr0poHrj-8C7Vz9d26HDyYgX2ofMcuF0eliP_uLCj50AyQWhK91-uVk1ThTy0qqs2$
>
> GPG Key ID = A46BEE1A
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
> VARNING: Klicka inte p? l?nkar och ?ppna inte bilagor om du inte k?nner
> igen avs?ndaren och vet att inneh?llet ?r s?kert.
> CAUTION: Do not click on links or open attachments unless you recognise
> the sender and know the content is safe.
>
>
>
>
>
>
>
>
>
> N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r
> det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r
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Message: 3
Date: Mon, 19 Jan 2026 10:58:18 +0000
From: Suyang Zhang <szhang at mrc-lmb.cam.ac.uk>
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] Postdoc position at MRC-LMB, Cambridge UK
Message-ID: <410D3062-B846-4C73-AC83-6A35213CED0C at mrc-lmb.cam.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Dear all,
My lab at the MRC-LMB in Cambridge is recruiting a postdoc to work on transcription-coupled splicing. We use a combined approach of structural biology (mainly cryo-EM), endogenous isolation, biochemistry and functional assays. Some of our recent work here 40624163 <https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/40624163/__;!!Mih3wA!D32cj_J-0w9icuZzC2W22Bxi_XVP0JJbyyu_hTyCV5eypKgPpvn0HWRtM9Qz72Vq9RAbiqHDQzXIz6JKYqTO6Raijg$ >, 40595577 <https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/40595577/__;!!Mih3wA!D32cj_J-0w9icuZzC2W22Bxi_XVP0JJbyyu_hTyCV5eypKgPpvn0HWRtM9Qz72Vq9RAbiqHDQzXIz6JKYqQJwYK1VQ$ >, 33446560 <https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/33446560/__;!!Mih3wA!D32cj_J-0w9icuZzC2W22Bxi_XVP0JJbyyu_hTyCV5eypKgPpvn0HWRtM9Qz72Vq9RAbiqHDQzXIz6JKYqQixB8ePg$ >.
We are seeking a candidate with a strong background in biochemistry or structural biology. Details of the postdoc position and how to apply can be found in the link below.
https://urldefense.com/v3/__https://mrc.tal.net/vx/mobile-0/appcentre-int/brand-3/spa-1/candidate/so/pm/1/pl/3/opp/2761-Postdoctoral-Researcher-Structural-Studies-Dr-Suyang-Zhang-LMB-2761/en-GB__;!!Mih3wA!D32cj_J-0w9icuZzC2W22Bxi_XVP0JJbyyu_hTyCV5eypKgPpvn0HWRtM9Qz72Vq9RAbiqHDQzXIz6JKYqRtYoIc4A$
Application deadline 11th Feb 2026.
Informal enquiries by email are welcome. Please feel free to contact me directly.
Best wishes,
Suyang
Suyang Zhang
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267077
https://urldefense.com/v3/__https://www2.mrc-lmb.cam.ac.uk/groups/zhang/__;!!Mih3wA!D32cj_J-0w9icuZzC2W22Bxi_XVP0JJbyyu_hTyCV5eypKgPpvn0HWRtM9Qz72Vq9RAbiqHDQzXIz6JKYqQVNfrd0A$
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