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

Tue Jul 5 07:26:05 PDT 2016

Dear Lu,

If you observe better upload via drive/dropbox, maybe the following would
be relevant?

"Aspera makes use of UDP transfer technology. Some institutes block the UDP
> port (port 33001) by default and it is not possible to get them enabled. If
> this is the case for you then we recommend that you use Globus which relies
> on GridFTP."
>

Have you given the alternative to Aspera a shot?

Is this apparent "throttling" of uploads specific to EMPIAR a common
experience with other list users? (please chime in!)

-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 10:15 AM, Lu Gan <lu at anaphase.org> wrote:

> Dear Ben,
>
> I can't speak for Rado, but I suspect many academics will have a similar
> problem: Universities may severely throttle your upload bandwidth. In our
> recent EMPIAR upload experience, we got 400 KB/sec max, independent of the
> upload client. This limitation was not due to our geographical location
> because I can get several MB/sec when using Google drive and sometimes
> Dropbox (when the latter is not being throttled).
>
>
> Cheers.
> Lu
>
> --
> Lu Gan
> Assistant Professor
> Department of Biological Sciences
> Centre for BioImaging Sciences
> National University of Singapore
> 14 Science Drive 4
> S1A, Lvl 2
> Singapore 117543
>
> www.anaphase.org
>
> Tel: (65) 6516 8868
> Fax: (65) 6776 7882
>
> On Tue, Jul 5, 2016 at 8:48 PM, Benjamin Himes <himes.benjamin at gmail.com>
> wrote:
>
>> 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 <%28412%29%20648-7262> *(Office)
>> *(412)648-8998 <%28412%29648-8998>* (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> wrote:
>>
>>> Send 3dem mailing list submissions to
>>>         3dem at ncmir.ucsd.edu
>>>
>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>         https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>> 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. 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>
>>> To: <3dem at ncmir.ucsd.edu>
>>> Subject: [3dem] Phase plate test dataset
>>> Message-ID: <08a401d1d698$9d39d0c0$d7ad7240$@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
>>>
>>> phone: +49 (89) 8578-2651
>>> fax: +49 (89) 8578-2641
>>>
>>> ===================================
>>>
>>>
>>>
>>>
>>>
>>> -------------- next part --------------
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>>> http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20160705/26bb81b7/attachment-0001.html
>>> >
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Tue, 5 Jul 2016 10:39:48 +0000
>>> From: Eric Gilles Hanssen <ehanssen at unimelb.edu.au>
>>> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
>>> Subject: [3dem] Postdoctoral position - Advanced Microscopy and
>>>         Modelling
>>> Message-ID: <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>
>>> 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://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
>>> 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>
>>> To: <3dem at ncmir.ucsd.edu>
>>> Subject: Re: [3dem] Phase plate test dataset
>>> Message-ID: <092301d1d6b9$2b29ab60$817d0220$@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
>>>
>>> user: MPIB
>>>
>>> pass: biochemie
>>>
>>>
>>>
>>> All the best,
>>>
>>>
>>>
>>> Rado
>>>
>>>
>>>
>>>
>>>
>>> From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Radostin
>>> Danev
>>> Sent: 05 July 2016 10:39
>>> To: 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
>>>
>>> phone: +49 (89) 8578-2651
>>> fax: +49 (89) 8578-2641
>>>
>>> ===================================
>>>
>>>
>>>
>>>
>>>
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>>> http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20160705/96ff3bba/attachment.html
>>> >
>>>
>>> ------------------------------
>>>
>>> Subject: Digest Footer
>>>
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>
>>>
>>> ------------------------------
>>>
>>> End of 3dem Digest, Vol 107, Issue 2
>>> ************************************
>>>
>>
>>
>> _______________________________________________
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