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Hi Tat, I thought it was the liquid nitrogen tank for the cooling system. We were thinking to have a better liquid nitrogen tank, which hopefulluy would maintain the temperature of the Aquilos-2 at -193 for multiple days.</div>
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Best</div>
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<p style="margin-top:0px; margin-bottom:0px">Chunyan Wang</p>
<div style="margin-top:0px; margin-bottom:0px"><span style="font-size: 15px; text-align: start; display: inline !important; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);">Microbial Sciences Institute</span><br style="font-size: 15px; text-align: start; color: rgb(32, 31, 30);">
<span style="font-size: 15px; text-align: start; display: inline !important; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);">Department of Microbial Pathogenesis</span><br style="font-size: 15px; text-align: start; color: rgb(32, 31, 30);">
<span style="font-size: 15px; text-align: start; display: inline !important; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);">Yale School of Medicine</span><br style="font-size: 15px; text-align: start; color: rgb(32, 31, 30);">
<span style="font-size: 15px; text-align: start; display: inline !important; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);">840 West Campus Drive</span><br style="font-size: 15px; text-align: start; color: rgb(32, 31, 30);">
<span style="font-size: 15px; text-align: start; display: inline !important; color: rgb(32, 31, 30); background-color: rgb(255, 255, 255);">New Haven, CT, 06516</span><br>
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1. Re: [+externe Mail+] Nitrogen support for Aquilos2<br>
(Cheng, Tat Cheung)<br>
<br>
<br>
----------------------------------------------------------------------<br>
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Message: 1<br>
Date: Thu, 6 Jul 2023 13:13:51 +0000<br>
From: "Cheng, Tat Cheung" <tatcheung.cheng@med.uni-goettingen.de><br>
To: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] [+externe Mail+] Nitrogen support for Aquilos2<br>
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<1956cadd-9698-4a06-e3b4-df77bcd962d1@med.uni-goettingen.de><br>
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Hi Chunyan,<br>
<br>
It doesn't cost much since it is just liquid nitrogen turned gas, if you mean by nitrogen cost. But if you mean by running fee of the system, then it varies between places.<br>
<br>
Tat<br>
<br>
<br>
On 06.07.23 14:39, Wang, Chunyan wrote:<br>
Hi Tat, that sounds great to be able to run Aquilos2 for multiple days. How much does that cost more or less ?<br>
Best<br>
<br>
<br>
Chunyan Wang<br>
<br>
Microbial Sciences Institute<br>
Department of Microbial Pathogenesis<br>
Yale School of Medicine<br>
840 West Campus Drive<br>
New Haven, CT, 06516<br>
________________________________<br>
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Today's Topics:<br>
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1. Re: [+externe Mail+] Re: Dry nitrogen generator that supports<br>
Aquilos cryo FIB (Cheng, Tat Cheung)<br>
2. DC EMI cancellation (Hannah Turner)<br>
3. Going from Amira filament picks to subtomogram averaging<br>
(Matthew Chang)<br>
4. Re: DC EMI cancellation (Andrzej ?ak)<br>
5. Post-doc in Paris (Kikuti Carlos)<br>
6. Re: DC EMI cancellation (Stahlberg Henning)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 5 Jul 2023 19:40:39 +0000<br>
From: "Cheng, Tat Cheung" <tatcheung.cheng@med.uni-goettingen.de><mailto:tatcheung.cheng@med.uni-goettingen.de><br>
To: "3dem@ncmir.ucsd.edu"<mailto:3dem@ncmir.ucsd.edu> <3dem@ncmir.ucsd.edu><mailto:3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] [+externe Mail+] Re: Dry nitrogen generator that<br>
supports Aquilos cryo FIB<br>
Message-ID:<br>
<d5f7acec-eb6c-0621-dfca-fbb6a3cb2626@med.uni-goettingen.de><mailto:d5f7acec-eb6c-0621-dfca-fbb6a3cb2626@med.uni-goettingen.de><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Xinran,<br>
<br>
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.<br>
<br>
Tat<br>
<br>
<br>
<br>
Multiscale Bioimaging Cluster of Excellence<br>
Fakult?t der Physik, D-1.111<br>
Friedrich-Hund-Platz 1, 37077 G?ttingen<br>
Telephon: +49 (0)551 / 39-60783<br>
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<br>
On 05.07.23 20:54, Sasha Dickinson wrote:<br>
Hi Xinran,<br>
<br>
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.<br>
<br>
Very best,<br>
Sasha<br>
<br>
On Wed, Jul 5, 2023 at 11:33?AM Liu, Xinran <xinran.liu@yale.edu<mailto:xinran.liu@yale.edu><mailto:xinran.liu@yale.edu><mailto:xinran.liu@yale.edu>> wrote:<br>
Dear Colleagues,<br>
<br>
I am looking for help to identify a dry N2 generator that can work with the Aquilos II cryo FIB (Thermo Fisher).<br>
<br>
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.<br>
<br>
N2 at connection of the microscope<br>
0.5x105 Pa (7.25 psi, 0.5 bar) to 0.8 x105 Pa (11.6 psi, 0.8 bar)<br>
Flow rate is 30 liters/min<br>
The water content must be less than 10 ppm<br>
<br>
Xinran Nick Liu, M.D. & Ph.D.<br>
Director, Center for Cellular & Molecular Imaging<br>
Electron Microscopy Core Facility<br>
Senior Research Scientist in Cell Biology<br>
Yale University School of Medicine<br>
Office Phone: 203.785.4050<br>
Lab Phone: 203.785.5390<br>
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Message: 2<br>
Date: Wed, 5 Jul 2023 20:05:54 +0000<br>
From: Hannah Turner <hannaht@scripps.edu><mailto:hannaht@scripps.edu><br>
To: "3dem@ncmir.ucsd.edu"<mailto:3dem@ncmir.ucsd.edu> <3dem@ncmir.ucsd.edu><mailto:3dem@ncmir.ucsd.edu><br>
Subject: [3dem] DC EMI cancellation<br>
Message-ID:<br>
<PH0PR11MB74707CAF6AE2A0BE4FA9B80FAC2FA@PH0PR11MB7470.namprd11.prod.outlook.com><mailto:PH0PR11MB74707CAF6AE2A0BE4FA9B80FAC2FA@PH0PR11MB7470.namprd11.prod.outlook.com><br>
<br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Dear Colleagues,<br>
<br>
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?<br>
<br>
Thank you,<br>
Hannah L. Turner<br>
Lab Manager, Andrew Ward Lab<br>
Scripps Research Institute, La Jolla CA, USA<br>
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<br>
Message: 3<br>
Date: Wed, 5 Jul 2023 10:30:41 -0400<br>
From: Matthew Chang <changmlw@umich.edu><mailto:changmlw@umich.edu><br>
To: 3dem@ncmir.ucsd.edu<<a href="mailto:3dem@ncmir.ucsd.edu">mailto:3dem@ncmir.ucsd.edu</a>><br>
Subject: [3dem] Going from Amira filament picks to subtomogram<br>
averaging<br>
Message-ID:<br>
<CAMZ7i9R9wvrpXw7dgU-65e0mzFnoxOJDC0p3Kx39HAdKPBB2nw@mail.gmail.com><mailto:CAMZ7i9R9wvrpXw7dgU-65e0mzFnoxOJDC0p3Kx39HAdKPBB2nw@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello all,<br>
<br>
I segmented filaments in Amira manually. I want to use that segmentation to<br>
extract coordinates with tilt and psi angle priors to do subtomogram<br>
reconstruction in Warp and subtomogram averaging in relion (using helical<br>
processing). Does anyone know if this is possible?<br>
<br>
Any help would be appreciated!<br>
<br>
Thank you,<br>
Matthew<br>
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Message: 4<br>
Date: Thu, 6 Jul 2023 08:31:52 +0200<br>
From: Andrzej ?ak <andrzej.zak@pwr.edu.pl><mailto:andrzej.zak@pwr.edu.pl><br>
To: Hannah Turner <hannaht@scripps.edu><mailto:hannaht@scripps.edu><br>
Cc: 3dem@ncmir.ucsd.edu<<a href="mailto:3dem@ncmir.ucsd.edu">mailto:3dem@ncmir.ucsd.edu</a>><br>
Subject: Re: [3dem] DC EMI cancellation<br>
Message-ID:<br>
<CAJqBd=eaYzhBPKFG9Hnx1=6FTqGjUMim1yXa4uEyQ350fLXDqQ@mail.gmail.com><mailto:CAJqBd=eaYzhBPKFG9Hnx1=6FTqGjUMim1yXa4uEyQ350fLXDqQ@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Hannah,<br>
I had such situation near the road, probably city start using other/more<br>
trams. The main reasons of DC are trams, trains, metros, elevators, etc. If<br>
pre measurement was taken during holidays, during the normal work day could<br>
be different (and getting worse in time, if anyone around mount some fancy<br>
equipment or you have more buildings and stuff around). As far as I know<br>
field cancelation like Spicer is the only way to go for DC. And nowadays<br>
it's good practice to mount it for any new TEM, just in case for the<br>
future.<br>
Best wishes<br>
Andrzej<br>
<br>
Andrzej ?ak, PhD Eng<br>
Wroclaw University of Science and Technology,<br>
tel. (+48)883314999<br>
e-mail: andrzej.zak@pwr.edu.pl<mailto:andrzej.zak@pwr.edu.pl><br>
<br>
?r., 5 lip 2023, 22:06 u?ytkownik Hannah Turner <hannaht@scripps.edu><mailto:hannaht@scripps.edu><br>
napisa?:<br>
<br>
> Dear Colleagues,<br>
><br>
><br>
><br>
> Has anyone had to correct for DC EMI after a site survey? Are there ways<br>
> to reduce or block occasional near DC peaks other than installing an entire<br>
> cancellation sytem?<br>
><br>
><br>
><br>
> Thank you,<br>
><br>
> Hannah L. Turner<br>
><br>
> Lab Manager, Andrew Ward Lab<br>
><br>
> Scripps Research Institute, La Jolla CA, USA<br>
> _______________________________________________<br>
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Message: 5<br>
Date: Thu, 6 Jul 2023 06:57:27 +0000<br>
From: Kikuti Carlos <Carlos.Kikuti@curie.fr><mailto:Carlos.Kikuti@curie.fr><br>
To: "CCPEM@jiscmail.ac.uk"<mailto:CCPEM@jiscmail.ac.uk> <CCPEM@jiscmail.ac.uk><mailto:CCPEM@jiscmail.ac.uk>,<br>
"3dem@ncmir.ucsd.edu"<mailto:3dem@ncmir.ucsd.edu> <3dem@ncmir.ucsd.edu><mailto:3dem@ncmir.ucsd.edu><br>
Subject: [3dem] Post-doc in Paris<br>
Message-ID: <20DF0C54-FF62-45A4-8859-50304D20FEEC@curie.fr><mailto:20DF0C54-FF62-45A4-8859-50304D20FEEC@curie.fr><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
The Structural Motility team, directed by Anne Houdusse at the Curie Institute (Paris Center), is searching for a post-doctoral fellow.<br>
<br>
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.<br>
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.<br>
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.<br>
Contact : Anne Houdusse (anne.houdusse@curie.fr<mailto:anne.houdusse@curie.fr><mailto:anne.houdusse@curie.fr><mailto:anne.houdusse@curie.fr>)<br>
Website : Structural Motility Team <a href="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!CovR4RnUmtyAvCWcnMNLt1FLaUX_xs7elBx5clWkzoBgoiB_pTnHY5h6_xCh4q0-cHGL4K4r1o3GFa7ec7PAaEdTI6EEQyQSo3iP3KCMyw$">
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Message: 6<br>
Date: Thu, 6 Jul 2023 08:16:12 +0000<br>
From: Stahlberg Henning <henning.stahlberg@epfl.ch><mailto:henning.stahlberg@epfl.ch><br>
To: Andrzej ?ak <andrzej.zak@pwr.edu.pl><mailto:andrzej.zak@pwr.edu.pl>, Hannah Turner<br>
<hannaht@scripps.edu><mailto:hannaht@scripps.edu><br>
Cc: "3dem@ncmir.ucsd.edu"<mailto:3dem@ncmir.ucsd.edu> <3dem@ncmir.ucsd.edu><mailto:3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] DC EMI cancellation<br>
Message-ID: <CD9B987F-B840-44E3-92F3-775FC6A88E9F@epfl.ch><mailto:CD9B987F-B840-44E3-92F3-775FC6A88E9F@epfl.ch><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
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.<br>
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.<br>
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.<br>
<br>
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.<br>
<br>
Best wishes,<br>
Henning.<br>
<br>
Henning Stahlberg<br>
Laboratory of?Biological Electron Microscopy<br>
Institute of?Physics, School of?Basic Sciences, EPFL, and<br>
Dep. of Fund. Microbiology,?Faculty of Biology and Medicine, UNIL,?<br>
Cubotron, BSP421, 1015 Lausanne,?Switzerland<br>
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From: 3dem <3dem-bounces@ncmir.ucsd.edu><mailto:3dem-bounces@ncmir.ucsd.edu> on behalf of Andrzej ?ak <andrzej.zak@pwr.edu.pl><mailto:andrzej.zak@pwr.edu.pl><br>
Date: Thursday, 6 July 2023 at 08:32<br>
To: Hannah Turner <hannaht@scripps.edu><mailto:hannaht@scripps.edu><br>
Cc: 3dem <3dem@ncmir.ucsd.edu><mailto:3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] DC EMI cancellation<br>
<br>
Dear Hannah,?<br>
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.?<br>
Best wishes?<br>
Andrzej?<br>
Andrzej ?ak, PhD Eng<br>
Wroclaw University of Science and Technology,<br>
tel. (+48)883314999<br>
e-mail: <a href="mailto:andrzej.zak@pwr.edu.pl">mailto:andrzej.zak@pwr.edu.pl</a><br>
<br>
?r., 5 lip 2023, 22:06 u?ytkownik Hannah Turner <<a href="mailto:hannaht@scripps.edu">mailto:hannaht@scripps.edu</a>> napisa?:<br>
Dear Colleagues,<br>
?<br>
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?<br>
?<br>
Thank you,<br>
Hannah L. Turner<br>
Lab Manager, Andrew Ward Lab<br>
Scripps Research Institute, La Jolla CA, USA<br>
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Subject: Digest Footer<br>
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End of 3dem Digest, Vol 191, Issue 9<br>
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