[ccp4bb] Research associate / Group leader position at the University of Luebeck (Northern Germany)

[Thomas Krey]

The Institute of Biochemistry (Director: Univ.-Prof. Dr. Thomas Krey) at the 
University of Luebeck has an opening for a position as a

Research associate / Group leader (m/w/d)

in full-time (currently 38.7 hours per week) for an initial period of 4 years. 
Within the position, the opportunity for further qualification (habilitation) 
is given.

Main areas of activity:

  *   Own research (incl. acquisition of third-party funding) on topics in 
structural infectiology
  *   Supervision of technical assistants, bachelor, master and doctoral theses
  *   Co-responsibility for the cryo-electron microscope planned at the site
  *   Organisation and implementation of teaching (in English) in biochemistry 
for the Molecular Life Sciences programme (lectures, practicals, seminars, 
performance review and booking, preparation of certificates)
  *   Participation in teaching (in German) in biochemistry for medical 
students (lectures, practicals, seminars and their performance review and 
booking)

Requirements:

  *   Completed university degree in a natural science or medical programme, 
e.g. biochemistry, molecular life sciences, chemistry or biology.
  *   Completed or nearly completed PhD thesis in natural sciences (defense in 
2022), preferably in the field of structural infectiology
  *   Proven research focus in the field of structural infectiology
  *   Experience in the field of cryo-electron microscopy
  *   Experience in teaching natural sciences and/or human medicine (in German 
and English)

More information can be found here

https://www.biochem.uni-luebeck.de/fileadmin/files/pdf/Ausschreibung1043-22_english.pdf

Please contact Prof. Dr. Thomas Krey (k...@biochemie.uni-luebeck.de) for any 
further questions, and send your written application with the usual documents 
(cover letter with research interests, curriculum vitae, references) summarised 
in a single PDF document by July 4th, 2022 (date of receipt) at the latest to 
bewerb...@uni-luebeck.de, quoting the reference number 1043/22.


Best wishes
Thomas


Prof. Dr. Thomas Krey
Hannover Medical School
Institute of Virology
Structural Virology Group
Carl-Neuberg-Str. 1
D-30625 Hannover
phone: +49 (0) 511 - 532 4308
email: krey.tho...@mh-hannover.de





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Re: [ccp4bb] Attention APS users - where will you go?

[Dr. Kevin M Jude]

Morning James, thanks for your attention to this issue.

I don’t mean to hijack your thread, but I’d also like to point out that here in 
the US, the proposed DOE FY2023 budget request includes cutting a 10% funding 
*cut* to X-ray light sources (based on 2018 baseline). It seems the timing 
couldn’t be worse, so I am pasting below a call to action that was shared with 
the SSRL user group:

Dear Colleagues:

I write to you as a member of the Stanford Synchrotron Radiation Lightsource 
(SSRL) user community to solicit your support for SSRL and the other Department 
of Energy (DOE) Basic Energy Sciences (BES) - funded X-ray light sources in the 
face of a potential cut in funding for facility operations. The cut in funding 
was proposed in the DOE’s FY2023 Presidential Budget Request (PBR) and, if 
enacted, would support only 90% of optimum, based on a 2018 baseline for SSRL 
and the other DOE BES X-ray Light sources.

If this email has reached you in error, then I apologize, but if not then 
please read on.

Thank you for your attention,

Graham George, Chair, Users’ Executive Committee, Stanford Synchrotron 
Radiation Lightsource

Attachments:

  1.  Separate copy of this message (pdf)
  2.  May 25th 2022 Letter sent to House and Senate Chairs and Ranking Members 
of Energy and Water subcommittees (pdf)
  3.  Example letter – please edit –  (MS Word)
Professor Graham N. George, B.Sc., D.Phil., D.Sc., FRSC(UK), FRSC
Molecular and Environmental Sciences Group, University of Saskatchewan


The issue: This DOE response to the FY2023 PBR stipulates that all five 
DOE-funded light sources (ALS, APS, NSLS-II, SSRL and LCLS) will be supported 
at approximately 90% of optimum level, with funding levels for normal 
operations based on a 2018 baseline. This proposed cut adds to the considerable 
deficit that has accumulated across the DOE-funded light source complex since 
the 2008 financial crisis. For example, between FY2018 and FY2022, facility 
operating budgets have increased at less than half the rate of inflation. As a 
result, facilities have already been forced to reduce scientific staffing 
levels to well below the optimum. Remaining staff are increasingly overworked 
in close to an unsustainable fashion, and this may lead to the mothballing of 
beamlines in FY2023. Given the importance of light sources in the modern 
scientific research environment, a direct consequence is severe erosion of US 
scientific competitiveness on the international stage. This impact will become 
dramatically worse should the trend not be rectified by a substantial increase 
in facility operating budgets.

What you are asked to do: We are asking users to telephone and write their 
elected representatives. This is especially important for users who are from 
states with members in the House and Senate who are on the Energy and Water 
Subcommittees. Please examine the membership to see if this is you, and if so 
then please act soon.

Senate: The membership list of the Senate subcommittee on Energy and Water 
Development is given at the following URL:
https://www.appropriations.senate.gov/subcommittees/energy-and-water-development
Telephone numbers are listed here: 
https://www.senate.gov/general/resources/pdf/senators_phone_list.pdf

House: The membership list House subcommittee on Energy and Water Development, 
and Related Agencies is given at the following URL:
https://appropriations.house.gov/subcommittees/energy-and-water-development-and-related-agencies-117th-congress
Telephone numbers, arranged alphabetically by location, are listed here: 
https://www.house.gov/representatives

Telephone Contact: This is an especially important mechanism because it is easy 
to do and because all telephone calls must be logged, whereas letters may not 
always be read. This is important if your representative serves on the House or 
Senate Energy and Water Subcommittees. Here is some advice for an effective 
telephone call:

  *   Be brief
  *   Identify yourself and your position (faculty, grad student, etc.) and 
that you are a constituent
  *   Indicate the importance of the Department of Energy X-ray light sources 
for your work
  *   Recognize the past support from Congress for scientific research then 
indicate your concern about the operating budget cut
  *   If you leave a voicemail leave your complete address
  *   Avoid acronyms as staff may not know what these mean
  *   If you talk to an individual make a note of the name of the person
  *   Make a note of the date and time that you called
Writing to your representative: If you are from a state with a committee 
member, then write to them and copy both the committee chairperson and the 
ranking member. Letters can be communicated by email; the information for which 
can be found on your member’s web site. If your state does not have 
representation on the subcommittee then write to the chairperson and the 
ranking member:

  *   Start with the issue in the first sentence of the 

Re: [ccp4bb] Attention APS users - where will you go?

[James Holton]

Thank you everyone who responded to my little poll.  To summarize and 
paraphrase, most common response was:

"I haven't really thought about it."

A distant second place was:
"I don't collect data at APS, so I'll be fine. (aka I'm not worried 
about all those APS users out-competing me for time at my favorite beamline)



and 3rd/4th place:
"I will go 'somewhere else' "
and/or
"we have an old rotating anode we can dust off."

Noteworthy responses I did NOT get were:
"I will just use cryoEM instead for a year or two"
nor
"I will just use AlphaFold "

With all due respect to the amazing recent advances in those fields, it 
would appear X-rays still play an important role in structural science, 
and a year of no data doesn't seem to be an option for most labs.


However, it would appear there is not much concern in the community.  
Personally, I wonder if that is justified. From what I can tell looking 
at public-facing calendars, most MX beamlines are being used about 80% 
of the time, and the APS represents at least half of total capacity in 
the USA. So, in April, I expect demand will rise to ~160% of supply. 
That means ~60% of beam time request proposals will get turned down.


To try and help illustrate, we at ALS have been pasting together a 
master calendar we call the "fly chromosome chart" here:

https://als-enable.lbl.gov/wordpress/2022/05/19/dark-period/

The width of the bars is proportional to the number of beamlines 
available.  Yes, they vary widely in flux and other capabilities, but 
assignment of beam time is usually done in "shifts".  Now, try to 
picture next year when the "APS" bar is all black.  Also, what kind of 
pins and pucks do you use? For many beamlines you may have to buy 
different ones.


Looking forward to the June 21 APS/U town hall discussions, as well as 
the ACA's "Bridging the APS dark period" session.  We will definitely be 
discussing this at the Diffraction Methods GRC, which is July 24-29, 
2022.  Space is still available!


-James Holton
MAD Scientist



On 5/9/2022 3:12 PM, James Holton wrote:

Greetings all,

I was just thinking of taking a little poll. When the Advanced Photon 
Source at Argonne shuts down for the APS-U upgrade on April 17, 2023, 
it will take with it about 90,000 hours of X-ray beam time until well 
into 2024. So, if you are a routine user of APS, what are your plans?  
Will you just stop collecting X-ray data for 12 months or so? Do you 
have a proposal lined up at another synchrotron? Is it in the USA? 
Europe? Asia? Or are you, like me, a big procrastinator and haven't 
really thought much about it?


Whatever it is, I'd like to hear from you. Either on- or off-list is 
fine. I expect this community will be interested in the digest.


-James Holton
MAD Scientist





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[ccp4bb] CBMS Lecture Series - June 15, 2022; 13:30 - Andrea Markelz - University of Buffalo

[Stojanoff, Vivian]

Please join us for ……



Andrea Markelz

University of Buffalo, SUNY



WEDNESDAY, June 15, 13:30 (EDT)



"Uncovering Protein Structural Dynamics with Terahertz Light"



Register in advance for this meeting:

https://bnl.zoomgov.com/meeting/register/vJItcOqurTssEgjFKexuOYLrWgcG4CkJUKo



Time conversion Link: 
https://www.worldtimebuddy.com/



Abstract:

The long-range structural vibrations of biomacromolecules (molecular weight > 
5kDa), are matched to biological thermal energies.  This intriguing overlap 
raises the question if, like sequence and structure, these dynamics are also 
evolutionarily optimized for robust and efficient biochemistry.  The vibrations 
for such massive systems are necessarily complex.  The structural vibrations 
involve displacements of entire subdomains, are numerous and closely spaced in 
energy, leading to dense spectra.  The spectra are further complicated by the 
energy overlap with collective excitations of the biological water necessary 
for in vivo structure and biological relevance.  Compounded with these effects, 
while a single spectrum corresponds to a single structure, biomacromolecular 
structure thermally samples small configurational changes in time, leading to 
variation in the vibrational spectra.  These effects all lead to the smooth 
featureless spectra seen by investigators for macroscopic samples. In this talk 
I will provide an overview of terahertz biomolecular studies and discuss the 
fundamental issue of isolating vibrational excitations based on specific 
structural displacements.  An example of a technique to provides this isolation 
is anisotropic terahertz microspectroscopy (ATM).  Using ATM we have found that 
indeed there are biases in the directionality of vibrational displacements 
which change with ligand binding and photoexcitation.  In particular 
photoexcitation measurements of orange carotenoid protein (OCP) demonstrate 
that intermediate states of the photo cycle coincide with changes in the 
directionality of vibrations, suggesting these reorganizations of the dynamics 
may assist with access to intermediate state structures.  Finally, I will 
discuss the challenges of current instrumentation, computational tools and 
sample preparation that need to be addressed to more fully realize the 
potential of THz in the understanding of the role of picosecond structural 
dynamics in biology.



















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[ccp4bb] Get funding to access Instruct-ERIC structural biology services via ISIDORe

[ccp4mail]

 Dear all,


ISIDORe launched the first call for transnational access for projects focusing 
on SARS-CoV-2 research.

Get access free of charge to cutting-edge services & technologies for 
structural biology and other services via ISIDORe.

ISIDORe supports access free of charge which includes logistical, technological 
and scientific support and, when appropriate, the specific training that is 
needed to use the services provided by the research facilities. Contribution to 
travel, accommodation and sample shipping will be offered.


Start your Pre Application 
here

  *   All scientists from Academia and Industry from European and non-European 
countries are eligible for this call.
  *   This call supports transnational access: scientists can only apply to 
services outside of their country of residence.
  *   The call supports physical, remote and virtual access to ISIDORe services
  *   The call will remain open as long as funding is available

[cid:3917691e-3764-4b90-8a38-bfa09358b428]



Application process:

1) Select your structural biology service of interest on the ISIDORe 
website
2) Fill in the pre-application form at the bottom of the service page (you will 
need an ORCID number to apply to this call)
3) You will receive an email with an ISIDORe ID number and a second email with 
a link towards the structural biology services application page.
4) On the application page, select the structure biology service(s) that you 
want to use, and apply for access via ARIA. You will need to provide the 
ISIDORe ID number in your application.


Get additional information about ISIDORe and the 1st transnational call on our 
ISIDORe help 
page.
 If you have any questions regarding ISIDORe and the call application process:


Contact Us




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[ccp4bb] Memrbane Structural Biology and characterization position at the Technical University of Denmark

[Jens Preben Morth]

Dear Colleagues,

There is an opening for a post doc position at the Technical University in 
Denmark
Check out this link for more information
https://www.dtu.dk/om-dtu/job-og-karriere/ledige-stillinger/job?id=df8299c8-5e73-4e7b-94c4-f4e3a0ba80d5

Best Preben

Best regards

J. Preben Morth

Professor


DTU Bioengineering



Technical University of Denmark

Department of Biotechnology and Biomedicine

Søltofts Plads

Building 224, Room 128

2800 Kgs. Lyngby

pr...@dtu.dk

www.dtu.dk/english












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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Rafal Dolot]

Dear CCP4 Users,

Thank you very much for all suggestions. Special thanks to Oliver for 
the ready-to-use files. Great job :) Hopefully it will solve my 
problems...


Best wishes,

Rafal
--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



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