[3dem] Nitrogen support for Aquilos2

Thu Jul 6 05:39:43 PDT 2023

Hi Tat, that sounds great to be able to run Aquilos2 for multiple days. How much does that cost more or less ?
Best

Chunyan Wang

Microbial Sciences Institute
Department of Microbial Pathogenesis
Yale School of Medicine
840 West Campus Drive
New Haven, CT, 06516
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Today's Topics:

   1. Re: [+externe Mail+] Re: Dry nitrogen generator that supports
      Aquilos cryo FIB (Cheng, Tat Cheung)
   2. DC EMI cancellation (Hannah Turner)
   3. Going from Amira filament picks to subtomogram averaging
      (Matthew Chang)
   4. Re: DC EMI cancellation (Andrzej ?ak)
   5. Post-doc in Paris (Kikuti Carlos)
   6. Re: DC EMI cancellation (Stahlberg Henning)

----------------------------------------------------------------------

Message: 1
Date: Wed, 5 Jul 2023 19:40:39 +0000
From: "Cheng, Tat Cheung" <tatcheung.cheng at med.uni-goettingen.de>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] [+externe Mail+] Re: Dry nitrogen generator that
        supports Aquilos cryo FIB
Message-ID:
        <d5f7acec-eb6c-0621-dfca-fbb6a3cb2626 at med.uni-goettingen.de>
Content-Type: text/plain; charset="utf-8"

Hi Xinran,

We also don't have house N2 gas. What we do is to use the gas outlet from a Taylor-Wharton 250L liquid nitrogen tank, with a higher pressure regulator (set to 6 bar max). It is not a standard usage of the tank, but it works for us. One thing to note is the cold N2 gas outlet needs to be warmed up to prevent crazy condensation. One tank lasts more than 1 week. While it may be hard to measure the water content in the N2 gas outlet, and it may depend on the cleanliness of the liquid N2, but our setup allows continuous usage of the Aquilos2 for multiple days.

Tat

Multiscale Bioimaging Cluster of Excellence
Fakult?t der Physik, D-1.111
Friedrich-Hund-Platz 1, 37077 G?ttingen
Telephon: +49 (0)551 / 39-60783
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On 05.07.23 20:54, Sasha Dickinson wrote:
Hi Xinran,

We also do not have house N2 gas so I tried a few different N2 sources and found that the best / most reasonable one was a standard ~5000 cubic feet tank at 350 PSI (as opposed to the typical 22 PSI). This tank usually lasts us >1 week on our Aquilos 2, so I usually have it replaced weekly like the ones for the cryoTEMs.

Very best,
Sasha

On Wed, Jul 5, 2023 at 11:33?AM Liu, Xinran <xinran.liu at yale.edu<mailto:xinran.liu at yale.edu>> wrote:
Dear Colleagues,

I am looking for help to identify a dry N2 generator that can work with the Aquilos II cryo FIB (Thermo Fisher).

It has become a concern that the Aquilos milling operation requires a huge volume of dry nitrogen that makes use of typical cylinders not practical. Because our building does not have a N2 supply source, we will have to purchase and install one that works with the Aquilos. Our multiple attempts to reach out to Thermo Fisher have not generated any response so far. The following are requirements for the generator, if someone here knows one or uses one that meet the criteria, can you share the information? much appreciated.

N2 at connection of the microscope
0.5x105 Pa (7.25 psi, 0.5 bar) to 0.8 x105 Pa (11.6 psi, 0.8 bar)
Flow rate is 30 liters/min
The water content must be less than 10 ppm

Xinran Nick Liu, M.D. & Ph.D.
Director, Center for Cellular & Molecular Imaging
Electron Microscopy Core Facility
Senior Research Scientist in Cell Biology
Yale University School of Medicine
Office Phone: 203.785.4050
Lab Phone: 203.785.5390
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------------------------------

Message: 2
Date: Wed, 5 Jul 2023 20:05:54 +0000
From: Hannah Turner <hannaht at scripps.edu>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: [3dem] DC EMI cancellation
Message-ID:
        <PH0PR11MB74707CAF6AE2A0BE4FA9B80FAC2FA at PH0PR11MB7470.namprd11.prod.outlook.com>

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Dear Colleagues,

Has anyone had to correct for DC EMI after a site survey? Are there ways to reduce or block occasional near DC peaks other than installing an entire cancellation sytem?

Thank you,
Hannah L. Turner
Lab Manager, Andrew Ward Lab
Scripps Research Institute, La Jolla CA, USA
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------------------------------

Message: 3
Date: Wed, 5 Jul 2023 10:30:41 -0400
From: Matthew Chang <changmlw at umich.edu>
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] Going from Amira filament picks to subtomogram
        averaging
Message-ID:
        <CAMZ7i9R9wvrpXw7dgU-65e0mzFnoxOJDC0p3Kx39HAdKPBB2nw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello all,

I segmented filaments in Amira manually. I want to use that segmentation to
extract coordinates with tilt and psi angle priors to do subtomogram
reconstruction in Warp and subtomogram averaging in relion (using helical
processing). Does anyone know if this is possible?

Any help would be appreciated!

Thank you,
Matthew
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Message: 4
Date: Thu, 6 Jul 2023 08:31:52 +0200
From: Andrzej ?ak <andrzej.zak at pwr.edu.pl>
To: Hannah Turner <hannaht at scripps.edu>
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] DC EMI cancellation
Message-ID:
        <CAJqBd=eaYzhBPKFG9Hnx1=6FTqGjUMim1yXa4uEyQ350fLXDqQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Hannah,
I had such situation near the road, probably city start using other/more
trams. The main reasons of DC are trams, trains, metros, elevators, etc. If
pre measurement was taken during holidays, during the normal work day could
be different (and getting worse in time, if anyone around mount some fancy
equipment or you have more buildings and stuff around). As far as I know
field cancelation like Spicer is the only way to go for DC. And nowadays
it's good practice to mount it for any new TEM, just in case for the
future.
Best wishes
Andrzej

Andrzej ?ak, PhD Eng
Wroclaw University of Science and Technology,
tel. (+48)883314999
e-mail: andrzej.zak at pwr.edu.pl

?r., 5 lip 2023, 22:06 u?ytkownik Hannah Turner <hannaht at scripps.edu>
napisa?:

> Dear Colleagues,
>
>
>
> Has anyone had to correct for DC EMI after a site survey? Are there ways
> to reduce or block occasional near DC peaks other than installing an entire
> cancellation sytem?
>
>
>
> Thank you,
>
> Hannah L. Turner
>
> Lab Manager, Andrew Ward Lab
>
> Scripps Research Institute, La Jolla CA, USA
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
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>
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Message: 5
Date: Thu, 6 Jul 2023 06:57:27 +0000
From: Kikuti Carlos <Carlos.Kikuti at curie.fr>
To: "CCPEM at jiscmail.ac.uk" <CCPEM at jiscmail.ac.uk>,
        "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: [3dem] Post-doc in Paris
Message-ID: <20DF0C54-FF62-45A4-8859-50304D20FEEC at curie.fr>
Content-Type: text/plain; charset="us-ascii"

The Structural Motility team, directed by Anne Houdusse at the Curie Institute (Paris Center), is searching for a post-doctoral fellow.

This dynamic laboratory is looking for an expert in sample preparation and structural determination via cryoEM studies. We use a multi-disciplinary approach combining structural biology (x-ray and cryoEM), chemical biology and cell biology to innovate in the investigation and understanding of molecular mechanisms involving different motors in cells. Our studies concern the very basics of force production, as well as the different cellular roles of the motors, their regulation, and how they can be targeted for developing novel chemical biology tools and therapies against human diseases.
 We are looking to recruit and train a dynamic and motivated candidate who is eager to gain independence and take the lead on one of our exciting scientific projects. Experience in sample preparation for cryoEM is essential. Experience in data processing, X-ray crystallography, molecular dynamics or cell biology is a plus.
 If you are interested, please send a CV and a statement of research interests and goals as well as three letters of recommendation from your previous employers.
Contact : Anne Houdusse (anne.houdusse at curie.fr<mailto:anne.houdusse at curie.fr>)
Website : Structural Motility Team https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Finstitut-curie.org*2Fteam*2Fhoudusse__*3B!!Mih3wA!Hf9w-ttvBHK5gtdM-qUvvGg3ZI5VUJDI044eyurC9Z6mlRfTyZTyqlY5SM8y-SYMoCJhChwWRG9fjFXUyOsz0SMjS58*24&data=05*7C01*7Cchunyan.wang.cw785*40yale.edu*7C91bc1a7b767a4e026de808db7df95db7*7Cdd8cbebb21394df8b4114e3e87abeb5c*7C0*7C0*7C638242282236502146*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=pOSqez*2Ff*2Fo4aY17KRd9y4*2Fh9m8ccFuYW1a*2F8m1C9NKI*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!EvxWKverlAtBOnlM9cOOx0lxafFLSH0B4HmZUciJuZbcq_KKa48v1gpdRlJdPzH5hcLm6ku02AdvOxd3IxvfhSB6CUphMJQ$ <https://urldefense.com/v3/__https://institut-curie.org/team/houdusse__;!!Mih3wA!Hf9w-ttvBHK5gtdM-qUvvGg3ZI5VUJDI044eyurC9Z6mlRfTyZTyqlY5SM8y-SYMoCJhChwWRG9fjFXUyOsz0SMjS58$>

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Message: 6
Date: Thu, 6 Jul 2023 08:16:12 +0000
From: Stahlberg Henning <henning.stahlberg at epfl.ch>
To: Andrzej ?ak <andrzej.zak at pwr.edu.pl>, Hannah Turner
        <hannaht at scripps.edu>
Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] DC EMI cancellation
Message-ID: <CD9B987F-B840-44E3-92F3-775FC6A88E9F at epfl.ch>
Content-Type: text/plain; charset="utf-8"

Hi,
We had strong EM fields from a nearby metro on one side of the building and a DC cable running hundreds of amperes DC current close to the intended EM site on the other side of the building. DC field variations at the intended EM location were stronger than 4000nT, while you wish to keep that below 50nT.   DC fields decay linearly with the distance from the source cable, while AC fields decay with distance squared from the source cable. So, in a certain distance, DC fields are the remaining problem.
Fields can be shielded passively with annealed mu-metal, which is very expensive and in addition requires to install a room in a room, which swallows 20cm from each wall. After that, fields inside the mu-metal cage are homogeneous and easier to shield passively. But the price is very high.
Fields can also be shielded actively with Helmholtz coils in X, Y and Z, providing a counter-field that neutralizes the field at least for the one location in the room where the system's field sensor is. That works well for a TEM without energy filter, if the field sensor of that active cancellation system is close to the sample stage, where the sensitivity is the highest. If in addition you also need a low field in a post-column filter of that TEM, then an active two-sensor / two-coil-pair system might be an option, or you need to go for the much more expensive passive shield solution. The active cancellation system compensates fields from 0Hz up to 1000Hz for one location in the room. If fields are inhomogeneous, e.g., from a nearby cable, then active cancellation would correct at one spot in the room but make matters worse everywhere else in the room.

Working closely with the excellent Systron AG in Zurich, Switzerland, we decided to move the instruments as far away from the source as possible (about 12 m in this case), and then install only the active cancellation systems MR-3 by Stefan Mayer in each EM room. This was 40x cheaper than passive cancellation and didn't consume any space. It worked well, all 300kV instruments reach 1.2? or better on apoferritin, also the one with postcolumn filter, even though the latter will benefit from the better location into which we will move the instruments soon.

Best wishes,
Henning.

Henning Stahlberg
Laboratory of?Biological Electron Microscopy
Institute of?Physics, School of?Basic Sciences, EPFL, and
Dep. of Fund. Microbiology,?Faculty of Biology and Medicine, UNIL,?
Cubotron, BSP421, 1015 Lausanne,?Switzerland
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From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Andrzej ?ak <andrzej.zak at pwr.edu.pl>
Date: Thursday, 6 July 2023 at 08:32
To: Hannah Turner <hannaht at scripps.edu>
Cc: 3dem <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] DC EMI cancellation

Dear Hannah,?
I had such situation near the road, probably city start using other/more trams. The main reasons of DC are trams, trains, metros, elevators, etc. If pre measurement was taken during holidays, during the normal work day could be different (and getting worse in time, if anyone around mount some fancy equipment or you have more buildings and stuff around). As far as I know field cancelation like Spicer is the only way to go for DC. And nowadays it's good practice to mount it for any new TEM, just in case for the future.?
Best wishes?
Andrzej?
Andrzej ?ak, PhD Eng
Wroclaw University of Science and Technology,
tel. (+48)883314999
e-mail: mailto:andrzej.zak at pwr.edu.pl

?r., 5 lip 2023, 22:06 u?ytkownik Hannah Turner <mailto:hannaht at scripps.edu> napisa?:
Dear Colleagues,
?
Has anyone had to correct for DC EMI after a site survey? Are there ways to reduce or block occasional near DC peaks other than installing an entire cancellation sytem?
?
Thank you,
Hannah L. Turner
Lab Manager, Andrew Ward Lab
Scripps Research Institute, La Jolla CA, USA
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