[3dem] 3dem Digest, Vol 134, Issue 19
Elad Binshtein
elad.binshtein at vanderbilt.edu
Wed Oct 10 15:02:49 PDT 2018
Hi Bradford,
We have TF-20 that run on windows and have SerialEM on this PC for
auto-data collection.
We use it mainly for negative stain SPA/RCT but it can be use easily with
the 626 holder for cryo.
Best,
On Wed, Oct 10, 2018 at 4:38 PM <3dem-request at ncmir.ucsd.edu> wrote:
> Send 3dem mailing list submissions to
> 3dem at ncmir.ucsd.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.ncmir.ucsd.edu%2Fmailman%2Flistinfo%2F3dem&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7Cb93a5af55cf848d7e91408d62ef8c38a%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636748043312411139&sdata=jMLHCpwp1r%2BdGjb%2FLGBWjmfkb92KlJhqAouLXf%2Fdn%2Bw%3D&reserved=0
> or, via email, send a message with subject or body 'help' to
> 3dem-request at ncmir.ucsd.edu
>
> You can reach the person managing the list at
> 3dem-owner at ncmir.ucsd.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of 3dem digest..."
>
>
> Today's Topics:
>
> 1. Setting up a 200kV Tecnai with 4K Eagle for SPA: Worth
> bothering? (Ross, Bradford)
> 2. Re: Setting up a 200kV Tecnai with 4K Eagle for SPA: Worth
> bothering? (Grassucci, Robert)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Oct 2018 20:53:34 +0000
> From: "Ross, Bradford" <bradford.ross at botany.ubc.ca>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: [3dem] Setting up a 200kV Tecnai with 4K Eagle for SPA: Worth
> bothering?
> Message-ID:
> <
> B48A2601A4664A4AAF5A3D2F0E482801025E6088F4 at s-itsv-mbx05p.ead.ubc.ca>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello 3DEM Community,
>
> We have a 200kV Tecnai G2 LaB6 TEM equipped with an Eagle 4K camera, Gatan
> 626 cryo holder, and a Vitrobot Mk IV. This instrument gets used fairly
> routinely for Cryo TEM of lipid nanoparticles, ambient temp TEM Tomography,
> and HRTEM of various types of nanoparticles down to approx. 1.4A crystal
> lattice resolution.
>
> Lately I've been thinking about setting the system up to acquire single
> particle cryo EM data to expand our capabilities. However, I know that the
> newer systems such as Talos Arctica, Glacios, Krios etc. with direct
> electron detectors are far more capable than what we have. Further, our
> Tecnai is currently completely running in a Windows environment, so that
> complicates things a bit with the SPA software packages all running on
> Linux. Are there folks out there running similar systems for this purpose?
> Do you set the microscope PC up to dual boot with Linux for single particle
> acquisition, or use the support PC? I have no experience in single particle
> acquisition or analysis, but lots of experience doing low dose cryo TEM and
> tinkering with our lab equipment.
>
> In short, would it be worth the effort of reconfiguring the system to
> acquire datasets that may be sub-par by today's standards? Or perhaps a
> useful hands-on experience in learning about how cryo SPA works, and
> expanding the capability of our lab?
>
> Cheers,
> Bradford Ross
>
> Electron Microscopy Technician
> BioImaging Facility
> University of British Columbia
> Cunningham Building Rm. 64
> 2146 East Mall
> Vancouver, B.C.
> V6T 1Z4
>
> phone 604-822-6996
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.ncmir.ucsd.edu%2Fpipermail%2F3dem%2Fattachments%2F20181010%2Fb16aa466%2Fattachment-0001.html&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7Cb93a5af55cf848d7e91408d62ef8c38a%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636748043312411139&sdata=DB65trJzssOeSMW4TdqNKQNlEYi1Nlt7fsTN27tUv8U%3D&reserved=0
> >
>
> ------------------------------
>
> Message: 2
> Date: Wed, 10 Oct 2018 21:35:59 +0000
> From: "Grassucci, Robert" <rg2502 at cumc.columbia.edu>
> To: "Ross, Bradford" <bradford.ross at botany.ubc.ca>,
> "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Setting up a 200kV Tecnai with 4K Eagle for SPA:
> Worth bothering?
> Message-ID:
> <
> DM6PR02MB39454028563449FDBA41A8CA94E00 at DM6PR02MB3945.namprd02.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Bradford,
> The 2 data collection software that are most broadly used for SPA Leginon
> and SerialEM can be set up with a microscope running windows. I have seen
> SerialEM
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbio3d.colorado.edu%2FSerialEM%2F&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7Cb93a5af55cf848d7e91408d62ef8c38a%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636748043312411139&sdata=ggWd8%2F5hWDWWTitGU2LFZUKo3ZxF8TmBNmF53rXijDE%3D&reserved=0
> set up directly on a Tecnai running windows or on a separate PC
> controlling the camera and communicating with the microscope PC using a
> client program. Leginon is generally run on a separate Linux computer and
> communicates with the microscope using a client program as well but
> requires a bit more to set up since it is linked to a database. The
> particulars of that system are at:
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Femg.nysbc.org%2Fredmine%2Fprojects%2Fleginon%2Fwiki%2FLeginon_Homepage&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7Cb93a5af55cf848d7e91408d62ef8c38a%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636748043312411139&sdata=snVbeaFaby03yXXy3HwtdGQ7pImeBc5VbECGWBlIguA%3D&reserved=0
>
> Either system will work well for what you want to do but both require a
> bit of time to become comfortable with them Gatan (Latitude) and
> Thermofisher (EPU) also sell SPA programs but I am not sure if they will
> work with an eagle camera. The commercial systems may have a bit more
> direct support as you pay for it but both the SerialEM and Leginon folks
> are very quick to respond to any query. Good luck.
> Regards,
> Bob
>
>
>
> From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Ross,
> Bradford
> Sent: Wednesday, October 10, 2018 4:54 PM
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Setting up a 200kV Tecnai with 4K Eagle for SPA: Worth
> bothering?
>
> Hello 3DEM Community,
>
> We have a 200kV Tecnai G2 LaB6 TEM equipped with an Eagle 4K camera, Gatan
> 626 cryo holder, and a Vitrobot Mk IV. This instrument gets used fairly
> routinely for Cryo TEM of lipid nanoparticles, ambient temp TEM Tomography,
> and HRTEM of various types of nanoparticles down to approx. 1.4A crystal
> lattice resolution.
>
> Lately I've been thinking about setting the system up to acquire single
> particle cryo EM data to expand our capabilities. However, I know that the
> newer systems such as Talos Arctica, Glacios, Krios etc. with direct
> electron detectors are far more capable than what we have. Further, our
> Tecnai is currently completely running in a Windows environment, so that
> complicates things a bit with the SPA software packages all running on
> Linux. Are there folks out there running similar systems for this purpose?
> Do you set the microscope PC up to dual boot with Linux for single particle
> acquisition, or use the support PC? I have no experience in single particle
> acquisition or analysis, but lots of experience doing low dose cryo TEM and
> tinkering with our lab equipment.
>
> In short, would it be worth the effort of reconfiguring the system to
> acquire datasets that may be sub-par by today's standards? Or perhaps a
> useful hands-on experience in learning about how cryo SPA works, and
> expanding the capability of our lab?
>
> Cheers,
> Bradford Ross
>
> Electron Microscopy Technician
> BioImaging Facility
> University of British Columbia
> Cunningham Building Rm. 64
> 2146 East Mall
> Vancouver, B.C.
> V6T 1Z4
>
> phone 604-822-6996
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.ncmir.ucsd.edu%2Fpipermail%2F3dem%2Fattachments%2F20181010%2Fb29b8d2c%2Fattachment.html&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7Cb93a5af55cf848d7e91408d62ef8c38a%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636748043312411139&sdata=%2FA7ZfdPkmgdRKyB5W7mo%2FWfB%2FJkispLDC1Vmn3Weh3g%3D&reserved=0
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
>
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.ncmir.ucsd.edu%2Fmailman%2Flistinfo%2F3dem&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7Cb93a5af55cf848d7e91408d62ef8c38a%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636748043312411139&sdata=jMLHCpwp1r%2BdGjb%2FLGBWjmfkb92KlJhqAouLXf%2Fdn%2Bw%3D&reserved=0
>
>
> ------------------------------
>
> End of 3dem Digest, Vol 134, Issue 19
> *************************************
>
--
________________________________
Elad Binshtein, Ph.D.
Cryo-EM specialist - Senior Staff Scientist
Center for Structure Biology (CSB)
MCN Room 1207
Vanderbilt University
Nashville, TN
Office: +1-615-322-4671
Mobile: +1-615-481-4408
https://www.linkedin.com/in/elad-binshtein-6bb89428/
E-Mail: elad.binshtein at vanderbilt.edu <eladbi at gmail.com>
twitter @EladBinshtein
________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20181010/26a38044/attachment-0001.html>
More information about the 3dem
mailing list