[3dem] Ethane Condensation Dewar

[Michael Godfrin]

Hi Joshua and 3DEM,

We/NanoSoft have been making foam dewars that have the same exact geometry
as the Vitrobot ethane dewar.  It's made of a much more durable foam that
isn't brittle like the Vitrobot one.  We've made these for our use and for
some of our partners and they've been of a "nice prototype quality".  This
post makes us think there may be wider interest in having this to purchase,
in which case we would consider finalizing the design and start selling it.

We would sell the styrofoam parts (dewar + floating ring) for ~$350 and if
you wanted the accompanying metal parts (brass ethane cup, spider, ring for
grid buttons) with it, we'd package it all for  ~$900.  We've seen quotes
from Thermo Fisher for these items and they were $550 (foam parts) and
$2,000 (foam + metal parts).   If you think this would be interesting
please let us know.  If we receive an enthusiastic response we will likely
finalize and start offering - if we don't receive much of a reply, we will
not pursue this further.

Mike


*Michael Godfrin, PhD*
*President*

*NanoSoft*
1372 Main St.
Coventry, RI 02816
Cell: (401) 829-5527
www.nanosoftmaterials.com

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On Wed, Jan 22, 2020 at 1:38 AM <3dem-request at ncmir.ucsd.edu> wrote:

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> Today's Topics:
>
>    1. Ethane Condensation Dewar (Joshua Denson)
>    2. Re: Ethane Condensation Dewar (John Rubinstein)
>    3. Re: [ccpem] Relion 3.1 CtfRefine anisotropic magnification
>       (Marin van Heel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 21 Jan 2020 18:22:23 -0700
> From: Joshua Denson <josh.denson2 at gmail.com>
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Ethane Condensation Dewar
> Message-ID:
>         <
> CAOgs41Nz7NJrRq051Mu6RwdMqcC_8HeHREK1NkvaMX_kdfoEsA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello 3DEM community,
>
> Our lab is currently working to set-up a manual plunge freezing device as a
> cost effective alternative to grid preparation using the Vitrobot. We are
> currently working off of a design we found on Github out of Purdue
> University (referenced here a few times) that seems reasonable for our
> machine shop to manufacture.
>
> The one thing we are having difficulty finding is some kind of a
> stand-alone ethane condensation dewar. A temperature regulated device would
> be nice, but something similar to what is used on the Vitrobot would also
> work well.
>
> I was wondering if anyone would be able to direct me to a place that I
> could purchase one, or if there are any designs out there for getting one
> made, that would also be great.
>
> Best,
> Joshua
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> ------------------------------
>
> Message: 2
> Date: Wed, 22 Jan 2020 03:30:44 +0000
> From: John Rubinstein <john.rubinstein at utoronto.ca>
> To: Joshua Denson <josh.denson2 at gmail.com>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Ethane Condensation Dewar
> Message-ID: <67CBE0F9-B7AA-4F2C-8C53-91FB050D79D4 at utoronto.ca>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Joshua,
>
> For both our modified Mark III Vitrobot and our high-speed ultrasonic grid
> freezing device (https://journals.iucr.org/d/issues/2019/12/00/ih5001/)
> we use an aluminum cryogen container within an insulating container.
> In order to avoid ethane freezing near liquid nitrogen temperature we mix
> it with propane (from propane torch cylinders) according to Bill Tivol?s
> method (
> https://www.cambridge.org/core/journals/microscopy-and-microanalysis/article/an-improved-cryogen-for-plunge-freezing/C791DB9759F82173E83309E1F8935101
> )
>
> The aluminum part for our ultrasonic device was designed to fit into the
> small styrofoam boxes used by AbCam.
> The design files are here (let me know if you need a different format):
> https://github.com/johnrubinstein/SIOcontrol/tree/master/CAD_files
> The part can be made by CNC milling, which is available as a web service
> from several companies (or you may be able to do it in your machine shop).
>
> Best,
> John
>
>
> ?
> John Rubinstein
> Molecular Medicine Program
> The Hospital for Sick Children
> 686 Bay Street, Rm. 20-9705
> M5G 0A4
> (+001) 416-813-7255
> www.rubinsteinlab.org<http://www.rubinsteinlab.org>
>
>
>
> On Jan 21, 2020, at 8:22 PM, Joshua Denson <josh.denson2 at gmail.com<mailto:
> josh.denson2 at gmail.com>> wrote:
>
> Hello 3DEM community,
>
> Our lab is currently working to set-up a manual plunge freezing device as
> a cost effective alternative to grid preparation using the Vitrobot. We are
> currently working off of a design we found on Github out of Purdue
> University (referenced here a few times) that seems reasonable for our
> machine shop to manufacture.
>
> The one thing we are having difficulty finding is some kind of a
> stand-alone ethane condensation dewar. A temperature regulated device would
> be nice, but something similar to what is used on the Vitrobot would also
> work well.
>
> I was wondering if anyone would be able to direct me to a place that I
> could purchase one, or if there are any designs out there for getting one
> made, that would also be great.
>
> Best,
> Joshua
> _______________________________________________
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> ------------------------------
>
> Message: 3
> Date: Wed, 22 Jan 2020 03:37:23 -0300
> From: Marin van Heel <marin.vanheel at googlemail.com>
> To: "Haji-Ghassemi, Omid" <omidgh85 at mail.ubc.ca>, 3dem
>         <3dem at ncmir.ucsd.edu>,  ccpem at jiscmail.ac.uk
> Subject: Re: [3dem] [ccpem] Relion 3.1 CtfRefine anisotropic
>         magnification
> Message-ID:
>         <CAHgnXPWLumgR=8=
> 6nxtgLMp9+3zNux51pdxtJoBqV6SJDshWTQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Omid,
>
> We recently had a very complicated case of reference bias: using a
> rotationally-symmetric reference image to pick spherical viruses sounds a
> logical thing to do does'nt it? However, it actually caused the data set to
> split into two: We got two 3D reconstructions differing in size by 0.9%.
> It took me more than a week to understand that that disparity was caused
> primarily by the picking of elliptical particles (2.6% anisotropic
> magnification) using a rotationally-symmetric reference. It was a very
> tricky case of reference bias...  So don't expect me to explain the nitty
> gritty details in less than 10 lines of email. Bottom line: our correction
> algorithm (see paper) took fully care of it.  The underlying problem was
> that we had not seriously looked at anisotropy due to an entirely different
> issue that obscured the data: our Cs-corrected Krios suffered from wild
> unpredictable astigmatism fluctuations during data collection (up to 1
> micron!), for almost three months. Only after that issue was resolved did I
> even try to measure anisotropic magnification.
> Hope this helps,
>
> Marin
>
>
> On Tue, Jan 21, 2020 at 7:19 PM Haji-Ghassemi, Omid <omidgh85 at mail.ubc.ca>
> wrote:
>
> > Dear Marin,
> >
> >
> >
> > Hope your are doing well and thanks again for a memorable time in Brazil
> > ?. I apologize for the delay in response and I really appreciate your
> > suggestion. It makes sense that anisotropic magnification is best
> performed
> > on the initial movie stacks but I don?t think I completely comprehend
> how anistropic
> > magnification correction lead to bias during picking if it is done after
> > the initial processing (since the picking is now done anyway). Can you
> > clarify?
> >
> >
> >
> > Best,
> >
> > Omid
> >
> >
> >
> > *From:* Marin van Heel <marin.vanheel at googlemail.com>
> > *Sent:* January 17, 2020 8:54 AM
> > *To:* Haji-Ghassemi, Omid <omidgh85 at mail.ubc.ca>; 3dem <
> > 3dem at ncmir.ucsd.edu>; ccpem at jiscmail.ac.uk
> > *Subject:* Re: [ccpem] Relion 3.1 CtfRefine anisotropic magnification
> >
> >
> >
> > Dear Omid,
> >
> >
> >
> > Anisotropic magnification should be corrected first, even before any CTF
> > determination, since its presence messes up the defocus/astigmatism
> > assessment. The anisotropic magnification measurement is
> best/conveniently
> > performed on the movie data itself. It does not require any separate
> > calibration measurements since the water ring information is always
> present
> > in large cryo-EM datasets, and those contain all the necessary anisotropy
> > information. The Imagic procedures allow you to a posteriori correct
> > anistropic magnification even in "legacy" cryo-EM datasets. Depending on
> > how you perform the correction, the average pixel size may change, and
> > consistency is important. It is not a good idea to do this anisotropic
> > magnification correction as an "afterthought" at the late stages of
> > refinement since it may bias other intermediate processing steps like
> > particle picking.
> >
> > We have described the procedure extensively in:
> >
> >  Afanasyev P, Seer-Linnemayr C, Ravelli RBG, Matadeen R, De Carlo S,
> > Alewijnse B, Portugal RV, Pannu NS, Schatz M, van Heel M:
> *Single-particle
> > cryo-EM using alignment by classification (ABC): the structure of
> Lumbricus
> > terrestris hemoglobin*, *IUCrJ. **4* (2017) 678-694.
> >
> >
> >
> > Hope this helps,
> >
> >
> >
> > Marin van Heel
> >
> >
> >
> > On Tue, Dec 24, 2019 at 7:30 PM Haji-Ghassemi, Omid <
> omidgh85 at mail.ubc.ca>
> > wrote:
> >
> > Dear All,
> >
> >
> >
> > I recently tried estimating the anisotropic magnification via CtfRefine
> in
> > Relion 3.1 and I get the following warning once the run was finished:
> >
> > WARNING: Overall magnification of optics group #1 (opticsGroup1) differs
> > from the nominal pixel size by 1.92044 %.
> >
> > WARNING: This overall difference changes the actual pixel size of the
> > reconstruction!
> >
> >
> >
> > I also attached the resulting log pdf file.
> >
> > I then notice subsequent 3D refinement yielded strange 3D volume and
> > really poor data quality. I have refined this dataset before and I
> obtain a
> > resolution of ~-3.8-3.9 Ang. I also attempted to calibrate the pixel size
> > on a region of the map where the resolution is the highest, and my pixel
> > size seemed correct. The pixel size of the data is supposed to be around
> > 1.08 or 1.09.
> >
> >
> >
> > So my questions are as follows:
> >
> > 1. Up to what resolutions can the anisotropic magnification be detected?
> >
> > 2. If indeed the data suffers from some degree of pixel error or
> > magnification issues, do I need to adjust it manually before submitting
> the
> > next refinement job? I assumed the correction is already applied after
> the
> > CtfRefine job. If so where is this information recorded? The pixel size
> > remained the same in the .star file of the header.
> >
> > 3. How do I analyze the log file data? It was not clear to me from after
> > consulting the tutorial and the paper by Zivanov et al., 2019.
> >
> >
> >
> > Regards,
> >
> > Omid
> >
> > ---------------------------------------------------
> >
> > ---------------------------------------------------
> >
> > Omid Haji-Ghassemi, Ph.D.
> >
> > Postdoctoral Fellow
> >
> > Department of Biochemistry & Molecular Biology
> >
> > Faculty of Medicine
> >
> > University of British Columbia
> >
> > 2350 Health Sciences Mall
> >
> > Vancouver, BC, V6T 1Z3
> >
> > Canada
> >
> >
> >
> >
> > ------------------------------
> >
> > To unsubscribe from the CCPEM list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
> >
> >
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