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

Tue Jul 5 08:04:33 PDT 2016

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)

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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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When replying, please edit your Subject line so it is more specific
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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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