[3dem] 3dem Digest, Vol 107, Issue 2

Tue Jul 5 13:54:42 PDT 2016

Hi Rado,
Thanks for making this subset already available even before finishing your
paper! It will be very useful for many.
best, Sjors

> Hi Ben,
>
>
>
> After my Dropbox "crashed" I considered putting it on EMPIAR but this is
> an "unofficial" small subset of images. I will definitely deposit the
> complete dataset with the original movies once the paper is ready.
> Hopefully within a month.
>
>
>
> All the best,
>
>
>
> Rado
>
>
>
>
>
> From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Benjamin
> Himes
> Sent: 05 July 2016 14:49
> To: 3dem at ncmir.ucsd.edu
> Subject: Re: [3dem] 3dem Digest, Vol 107, Issue 2
>
>
>
> Dear Rado,
>
> Is there any reason in particular you elected to not share your data
> through the EMPIAR <https://www.ebi.ac.uk/pdbe/emdb/empiar/> ?
>
> "EMPIAR, the Electron Microscopy Pilot Image Archive, is a public resource
> for raw, 2D electron microscopy images. Here, you can browse, upload, and
> download and reprocess the thousands of raw, 2D images used to build a 3D
> structure."
>
> -Ben H.
>
>
>
>
> *************************************
>
> Benjamin Himes
>
> Department of Structural Biology
>
> University of Pittsburgh School of Medicine
> 2050 Biomedical Science Tower 3 (BST3).
>
> 3501 5th Ave, Pittsburgh, PA 15260
>
>
>
> (412) 648-7262 (Office)
>
> (412)648-8998 (Lab fax)
>
> *************************************
>
>
>
> No trees were killed to send this message, but
>
> a large number of electrons were terribly inconvenienced.
>
>
>
> It is an abiding passion of human beings to attempt to read and re-view
> history as an orderly progression of events running according to a
> well-coordinated and rational script. Don't be fooled.
>
>
>
>
>
> On Tue, Jul 5, 2016 at 8:32 AM, <3dem-request at ncmir.ucsd.edu
> <mailto:3dem-request at ncmir.ucsd.edu> > wrote:
>
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> Today's Topics:
>
>    1. Phase plate test dataset (Radostin Danev)
>    2. Postdoctoral position - Advanced Microscopy and Modelling
>       (Eric Gilles Hanssen)
>    3. Re: Phase plate test dataset (Radostin Danev)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 5 Jul 2016 10:38:33 +0200
> From: Radostin Danev <danev at biochem.mpg.de <mailto:danev at biochem.mpg.de> >
> To: <3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu> >
> Subject: [3dem] Phase plate test dataset
> Message-ID: <08a401d1d698$9d39d0c0$d7ad7240$@biochem.mpg.de
> <http://biochem.mpg.de> >
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Colleagues,
>
>
>
> As I mentioned at the 3DEM GRC I am happy to share a small subset of phase
> plate images acquired with defocus.
>
> I put the first 20 images of a 20S proteasome dataset on my Dropbox, here:
> https://www.dropbox.com/sh/omjjhwhhqsjvsm6/AAAAg32yTzc4_CvrjtdQI_Raa?dl=0
>
> There are also picked particle coordinates in *_automatch.star and CTF
> parameters in *_ctffind3.log files.
>
> Other data:
>
> - accel. voltage 300 kV
>
> - pixel size 1.054 A
>
> - Cs 2.62 mm
>
> - particle diameter 190 A
>
>
>
> With D7 symmetry this subset of ~ 7,300 particles refines to ~ 2.9 A
> resolution.
>
>
>
> All the best,
>
>
>
> Rado
>
>
>
>
>
> ===================================
>
> Radostin Danev, Ph.D.
>
> Max Planck Institute of Biochemistry
> Department of Molecular Structural Biology
> Am Klopferspitz 18
> 82152 Martinsried
> Germany
>
> e-mail: danev at biochem.mpg.de <mailto:danev at biochem.mpg.de>
>
> phone: +49 (89) 8578-2651 <tel:%2B49%20%2889%29%208578-2651>
> fax: +49 (89) 8578-2641 <tel:%2B49%20%2889%29%208578-2641>
>
> ===================================
>
>
>
>
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 5 Jul 2016 10:39:48 +0000
> From: Eric Gilles Hanssen <ehanssen at unimelb.edu.au
> <mailto:ehanssen at unimelb.edu.au> >
> To: "3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu> "
> <3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu> >
> Subject: [3dem] Postdoctoral position - Advanced Microscopy and
>         Modelling
> Message-ID: <4E057941-24F1-43B7-B41B-2D14A3263E9A at unimelb.edu.au
> <mailto:4E057941-24F1-43B7-B41B-2D14A3263E9A at unimelb.edu.au> >
> Content-Type: text/plain; charset="windows-1252"
>
> Dear all,
> The University of Melbourne is advertising in new post doctoral position
> for advanced imaging see below.
> Please contact Prof Leann Tilley for more info ltilley at unimelb.edu.au
> <mailto:ltilley at unimelb.edu.au> <mailto:ltilley at unimelb.edu.au
> <mailto:ltilley at unimelb.edu.au> >
> Regards
> Eric
>
> Postdoctoral Research Fellow ? Advanced Microscopy
> Department of Biochemistry and Molecular Biology, University of Melbourne
>
> This position is funded by an Australian Research Council Laureate
> Fellowship Program. The vision of the program is to develop sophisticated
> and integrated bio-metrology (measurement) methods to study a complex
> cellular processes in the malaria parasite. You will work with a team of
> experts to develop and implement novel imaging methods, biophysical
> techniques and computational studies that will enable, for the first time,
> whole organism mapping and modelling of malaria parasites. The Program
> will work as an interdisciplinary collaboration for high-resolution
> bio-imaging and computational modelling. The host laboratory is situated
> in the Bio21 Molecular Science and Biotechnology Institute, on the
> University campus. You will work with colleagues from the University?s
> Departments of Biochemistry and Molecular Biology, Maths and Stats and
> from the School of Engineering.
> Salary: $66,809* - $90,657 p.a. (*PhD Entry Level $84,458 p.a.) plus 9.5%
> superannuation
> Job No: 0041023
> For position information and to apply online go to
> http://about.unimelb<http://about.unimelb.edu.au/careers>.edu.au/careers
> <http://edu.au/careers> <http://about.unimelb.edu.au/careers>, and under
> the relevant option (?Current Staff? or ?Prospective Staff?) search by the
> job title or number.
> http://jobs.unimelb.edu.au/caw/en/job/888403/postdoctoral-research-fellow-advanced-microscopy
>
>
>
> Assoc/Prof Eric Hanssen
>
> Head - Bio21 Advanced Microscopy Facility
> Principle Fellow - Department of Biochemistry and Molecular Biology
>
> The University of Melbourne
> Bio21 Institute - 30 flemington rd - VIC 3010
> +61 3 8344 2449 <tel:%2B61%203%208344%202449>
> www.microscopy.unimelb.edu.au <http://www.microscopy.unimelb.edu.au>
> <http://www.microscopy.unimelb.edu.au>
>
>
>
>
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> ------------------------------
>
> Message: 3
> Date: Tue, 5 Jul 2016 14:31:35 +0200
> From: Radostin Danev <danev at biochem.mpg.de <mailto:danev at biochem.mpg.de> >
> To: <3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu> >
> Subject: Re: [3dem] Phase plate test dataset
> Message-ID: <092301d1d6b9$2b29ab60$817d0220$@biochem.mpg.de
> <http://biochem.mpg.de> >
> Content-Type: text/plain; charset="us-ascii"
>
> My Dropbox public links were suspended due to "excessive traffic". I
> uploaded the dataset to our FTP server (could be a bit slow):
>
>
>
> bmftp.biochem.mpg.de <http://bmftp.biochem.mpg.de>
>
> user: MPIB
>
> pass: biochemie
>
>
>
> All the best,
>
>
>
> Rado
>
>
>
>
>
> From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu
> <mailto:3dem-bounces at ncmir.ucsd.edu> ] On Behalf Of Radostin Danev
> Sent: 05 July 2016 10:39
> To: 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
> Subject: [3dem] Phase plate test dataset
>
>
>
> Dear Colleagues,
>
>
>
> As I mentioned at the 3DEM GRC I am happy to share a small subset of phase
> plate images acquired with defocus.
>
> I put the first 20 images of a 20S proteasome dataset on my Dropbox, here:
> https://www.dropbox.com/sh/omjjhwhhqsjvsm6/AAAAg32yTzc4_CvrjtdQI_Raa?dl=0
>
> There are also picked particle coordinates in *_automatch.star and CTF
> parameters in *_ctffind3.log files.
>
> Other data:
>
> - accel. voltage 300 kV
>
> - pixel size 1.054 A
>
> - Cs 2.62 mm
>
> - particle diameter 190 A
>
>
>
> With D7 symmetry this subset of ~ 7,300 particles refines to ~ 2.9 A
> resolution.
>
>
>
> All the best,
>
>
>
> Rado
>
>
>
>
>
> ===================================
>
> Radostin Danev, Ph.D.
>
> Max Planck Institute of Biochemistry
> Department of Molecular Structural Biology
> Am Klopferspitz 18
> 82152 Martinsried
> Germany
>
> e-mail: danev at biochem.mpg.de <mailto:danev at biochem.mpg.de>
>
> phone: +49 (89) 8578-2651 <tel:%2B49%20%2889%29%208578-2651>
> fax: +49 (89) 8578-2641 <tel:%2B49%20%2889%29%208578-2641>
>
> ===================================
>
>
>
>
>
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>
> End of 3dem Digest, Vol 107, Issue 2
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>
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>
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-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres