Re: [ccp4bb] DIALS 3.11 release: graphical utilities broken

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear all,

Updated release at https://dials.github.io/installation.html - 3.11.1 - now 
based on Python 3.9.13 - with  working graphical utilities

Sorry to those who stubbed their toes on this, many thanks to my colleagues for 
fixing this on 1st day back :-)

All the best Graeme

On 30 Aug 2022, at 16:31, Winter, Graeme (DLSLtd,RAL,LSCI) 
<6a19cead4548-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hello everyone including brave souls who are keen to use the latest greatest 
version of DIALS - the recently released 3.11

Sorry

Please don’t

We have had a couple of reports of issues with the graphical utilities in here 
caused by upstream changes in Python which have completely broken the graphical 
libraries on which we depend

Locally detailed at

https://github.com/dials/dials/issues/2216

For anyone who wants to see the gory details which are a side-effect of

https://github.com/python/cpython/issues/82180

As this is in our graphical interface tools it is not subject to automated 
testing and it would appear that those of us who are developing on 3.10 did not 
stumble across the problem

We will make a .1 release in the next couple of days - it would appear that the 
nightly builds are also affected by the same issue.

In the meantime I recommend people download the previous latest release 3.10.3

https://github.com/dials/dials/releases/tag/v3.10.3

I would like to emphasise that the algorithms are still fine (I believe) this 
is just an error with the viewers but fixing this in the longer term could be a 
substantial body of work.

For those who get their DIALS from CCP4 you will be fine as that is still on 
Python 3.7 or 3.8 so will not be affected by these issues.

Best wishes Graeme


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[ccp4bb] PhD thesis offer (F/M) "Structure of the vaccinia virus DNA replication machinery..."

[Wim Burmeister]

  
  
 We are looking for a PhD
student (f/m) starting on 1 November 2022 or on 1 January 2023
  in our team at the Institut de Biologie Structurale (IBS) in Grenoble, France working on the
Structure
of the vaccinia virus DNA replication machinery in complex with
DNA substrates by single-particle cryo-electron microscopy
With
  the recent spread of monkeypox infections, poxviruses got into the
  headlines. Our team works on the elucidation of structure and
  function of the poxvirus DNA replication machinery, now mainly by
  single-particle cryo-electron microscopy. The DNA replication of
  vaccinia virus, a safe model system, involves the DNA polymerase
  holoenzyme complex E9-A20-D4, furthermore the hexameric
  helicase-primase D5. The aim is to determine structures of these
  assemblies by cryo-EM with bound DNA substrates, nucleotides,
  inhibitors and nucleotide analogues in order to stabilize
  different functional states for the understanding of poxvirus DNA
  replication. The project builds on the team’s experiences in the
  structure determination and biophysical characterization of the
  partners and their domains, our recent results on the cryo-EM of
  the helicase domain of D5 and first results by cryo-EM on the
  holoenzyme. 
The
  candidate should be computer literate and have some experience in
  the use of Linux. Knowledge of relevant software packages used for
  cryo-EM will be an asset. Furthermore, a sound background in
  biochemistry, physics or biophysics is required as the project
  comprises multiple methods: protein production in the
  baculovirus-insect cell system; protein purification by affinity
  chromatography; sample preparation for cryo-EM. structure
  calculations for single-particle cryo-EM on a Linux computing
  cluster; analysis and visualization of protein structures.
The successful candidate will work in a small team interested in poxvirus DNA
replication directed by Prof. Wim
Burmeister within the « Viral Replication Machines group ». Cryo-EM and computing facilities are available
on the research campus, which is shared with international institutes: the EMBL Grenoble
outstation, the ESRF synchrotron and the ILL research
reactor. Working languages of the
institute are English and French. Grenoble is a mid-size
town with an international atmosphere located in the
middle of the French Alps. The net salary is about 1750 €/month (~2000 € gross salary),
In order to candidate please send a CV, a letter of
motivation and a copy of the Master diploma with marks to wim.burmeis...@ibs.fr
before 30 September, 2022.
Bibliography
Tarbouriech N, Ducournau C,
Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN,
Burmeister WP & Iseni F. The vaccinia virus DNA polymerase
structure provides insights into the mode of processivity factor
binding. Nat Commun. 2017;8: 1455.*
doi:10.1038/s41467-017-01542-z.
Bersch B, Tarbouriech N,
Burmeister WP, Iseni F. Solution structure of the C-terminal
domain of A20, the missing brick for the characterization of the
interface between vaccinia virus DNA polymerase and its
processivity factor. J Mol Biol. 2021; 167009.*
doi:10.1016/j.jmb.2021.167009.
Hutin, S., Ling, W.L.,
Tarbouriech, N., Schoehn, G, Grimm, G., Fischer, U. &
Burmeister, W.P. The vaccinia virus DNA helicase structure from
combined single-particle cryo-electron microscopy and AlphaFold2
prediction. Viruses. In press.
-- 
  
  
  Wim
Burmeister
  

  

  

  

  

  

   Professeur
  Institut
de Biologie Structurale (IBS) CIBB
  71
avenue des Martyrs / CS 20192
  
   38044 Grenoble Cedex 9,
  FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41  
Fax: +33 (0) 476 20 94 00
  website 
                                   
map
  
  
  Changement
climatique : «Les autres combats n’ont

[ccp4bb] FW: MRC Molecular and Cellular Medicine Board; Board Member Vacancy

[Martyn Winn - STFC UKRI]

Hi all. I'm forwarding this announcement on behalf of Robert Deller at the MRC:


As you may be aware, MRC conducts an annual recruitment exercise to fill 
vacancies across its boards and panels.

https://www.ukri.org/about-us/work-for-us/join-an-advisory-committee-panel-or-network/mrc-board-and-panel-vacancies/

The current recruitment exercise also includes a vacancy within the Molecular 
and Cellular Medicine Board focused on Structural Biology that I believe could 
appeal to individuals within the CCP4 community. The deadline for applications 
is the 30th September 2022.



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[ccp4bb] We are looking for a Assistant/Associate Professor in Cryogenic Electron Microscopy at the M4I, Maastricht University

[M4I]

Are you a researcher who aspires to develop further in the research of cryo-EM 
for structural (cellular) biology? Is your ambition to start your own research 
line, while consolidating and complementing our existing teams? If yes, then 
Maastricht University has a new challenge for you.


For the job description and more information on this position, please use the 
following link. There you have the possibility to apply for this interesting 
position before 25th of September 2022:
https://www.academictransfer.com/en/316956/assistantassociate-professor-in-cryogenic-electron-microscopy-at-the-m4i-maastricht-university/

Kind regards, | Met vriendelijke groet,

[cid:image001.png@01D5787A.84D82A40]

Anita Mühlegger
Personal Assistant M4I Nanoscopy
Faculty of Health, Medicine & Life Sciences
M4I - Maastricht MultiModal Molecular Imaging Institute
Universiteitssingel 50 | location: UNS50, K5.459 | 6229 ER Maastricht | PO Box 
616 | 6200 MD Maastricht
* +31 6 39 60 19 88 | 
pa-nanosc...@maastrichtuniversity.nl
Working days: Mon/Tue-all day | Thu-morning
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responsibility before printing this e-mail.




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[ccp4bb] Researcher2 position

[yeg University of Minnesota]

Dear all,

A researcher2 position is available at Dr. Fang Li lab UMN.

 *Researcher 2 position*

Applicants are invited to a Researcher 2 position in the Laboratory of
Structural Biology of Disease at the Department of Pharmacology, Medical
School, the University of Minnesota, headed by Dr. Fang Li (PI).



*Basic Qualifications*

·  A master's degree in Molecular Biology or related fields or a
bachelor's degree in Molecular Biology with 2+ years of relevant
experience.

·  Hands-on experiences include molecular cloning, mammalian cell
culture, protein expression and purification.

·  Innovation and self-motivation, capable of working independently and
in a team setting.

   - Excellent verbal and written communication skills

*Duties and Responsibilities:*

·  70% - Perform molecular biology and protein biochemistry experiments
to study virus entry into host cells. The incumbent will be supervised, but
he/she needs to learn to be independent.

·  30% - Assist with various administrative duties related to the
functioning of the laboratory.
Review of applications will start immediately and continue until the
position is filled. To apply, please submit your current CV, a research
statement, and two recommendation letters directly to Dr. Li (lif...@umn.edu).
More information about Dr. Li's lab can be found at
http://www.msi.umn.edu/~lifang.

Best,
Gang



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