[3dem] carbon coating devices
Wang, Tong
twang1 at gc.cuny.edu
Thu Jun 4 13:16:19 PDT 2020
Hi David,
We have ACE600 carbon coater (carbon rod) and metal sputter (Au) for several years. Carbon coater and thickness monitor work great and we are happy with the results. we use it for both thin continuous carbon films in cryoEM and carbon coating in SEM imaging. Our model has metal sputter coating for SEM imaging. Both carbon coating and sputter coating work great for SEM imaging. It does take a little long to prepare carbon rod which lasts several rounds of coating (3-5 nm). Consumables (carbon rods) are expensive and it is hard to find compatible ones. I have tried spec-pure carbon rods from Ted Pella (grade 1), EMS and 2SPI.com. Many of them cannot last one coating (5 nm). I called the tech support and was told I must use carbon rod from Leica.
Our model includes option of glow discharge. However we did not have good experience when using both glow discharge and sputter coating. We observed tiny black dots on carbon film after glow discharge. I suspect that sputter coating left metal layer on the inner surface of chamber and source shutter which might be sputtered during glow discharge. In the end we gave up glow discharge with this model.
Best,
Tong
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Today's Topics:
1. carbon coating devices (Morgan, David Gene)
2. Re: carbon coating devices (Ruben Diaz)
3. "Recenter" option in Relion during particle extraction
(Iozzo, Yuri /US)
----------------------------------------------------------------------
Message: 1
Date: Wed, 3 Jun 2020 21:22:41 +0000
From: "Morgan, David Gene" <dagmorga at indiana.edu>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: [3dem] carbon coating devices
Message-ID: <1591219361608.86480 at indiana.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
Does anyone have experience with the Leica ACE600 carbon coater/metal sputter coater? I am very wary of buying a dual purpose device like this as our only way to make carbon films for TEM grids, but I may be being overly cautious. If anyone has thoughts or experiences, please let me know.
--
politics is more difficult than physics.
A. Einstein
David Gene Morgan
Electron Microscopy Center
047E Simon Hall
IU Bloomington
812 856 1457 (office)
812 856 3221 (3200)
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Message: 2
Date: Wed, 3 Jun 2020 14:31:21 -0700
From: Ruben Diaz <pindusito at gmail.com>
To: "Morgan, David Gene" <dagmorga at indiana.edu>
Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] carbon coating devices
Message-ID:
<CAMUb-c6o-9Lf27MTNEc86SjCbdzvPqZarDeMe1=+ggfrX+xr+Q at mail.gmail.com>
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Hi David,
We have a spanking new one here at La Jolla Institute, so I cannot attest
to its reliability yet, but from my first two tries making the carbon, I
can tell you that the film releases beautifully from the mica sheets and
looks like a mirror. It is the nicest I have seen. In the microscope, the
film also looks super uniform and nice. Using the evaporator is very easy,
although the preparation takes a little longer than with a Cressington, for
example, or a Denton, and you need to have pretty steady hands for this
(don't drink too much coffee before doing it). The thickness monitor seems
to be spot on and the gadget looks gorgeous and shiny. We have the version
that also does sputtering, and you can do your glow discharge with it. On
the minus side, is the fact that it is rather pricey, and Leica parts (some
of which are consumables) are very expensive, but each carbon rod is
supposed to last for several shots.
Ruben,
On Wed, Jun 3, 2020 at 2:22 PM Morgan, David Gene <dagmorga at indiana.edu>
wrote:
> Hi,
>
>
> Does anyone have experience with the Leica ACE600 carbon coater/metal
> sputter coater? I am very wary of buying a dual purpose device like this
> as our only way to make carbon films for TEM grids, but I may be being
> overly cautious. If anyone has thoughts or experiences, please let me know.
>
>
> --
> politics is more difficult than physics.
> A. Einstein
>
> David Gene Morgan
> Electron Microscopy Center
> 047E Simon Hall
> IU Bloomington
> 812 856 1457 (office)
> 812 856 3221 (3200)
> https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!VULpcu2spEXZwHm0God9yWs1uBWR91_qyCEVRi1SnusTb6dcvuafJBlVnYIncpdLBA$
> <https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!UQ9Qrot0OBWFZRBfeQ73s2RYuHMDMGc9lAM5US2gCul9XQ4Mh_K-LuH5A41cqjuECg$>
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Message: 3
Date: Wed, 3 Jun 2020 22:14:48 +0000
From: "Iozzo, Yuri /US" <Yuri.Iozzo at sanofi.com>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: [3dem] "Recenter" option in Relion during particle extraction
Message-ID:
<MWHPR05MB367799C32051F77451FE2B31F9880 at MWHPR05MB3677.namprd05.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Hi everyone,
I wonder if someone can explain or can point me to a good description to understand the "recenter" option when you extract the particles in Relion. After years of use I am not sure what exactly it does.
Here is my experience with it:
* If I do not use any offsets for particle extraction and for my starting reference MRC file then I get a reconstruction usually close to the coordinates of starting reference,
* If I use XYZ (which represent the difference between voxel center and map's center of mass) offsets for extraction and still use the same starting reference then I get a perfectly centered reconstruction, although it is very distorted and compressed relative to what it should be,
* If I use XYZ offsets for extraction and also apply them to my starting reference (for example: "relion_image_handler --i reference.mrc --o reference_xyz.mrc --shift_x x --shift_y y --shift_z z" or "relion_image_handler --i reference.mrc --o reference_-xyz.mrc --shift_x -x --shift_y -y --shift_z -z") then the resulting reconstruction does not make any sense.
Is there any clear answer preferably with an example about when the Recenter option is useful?
Thanks,
Yuri Iozzo
Sanofi
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