[ccp4bb] School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic

2024-03-14 Thread Jan Dohnalek 
Dear colleagues,

We welcome registrations to a specialized course focused on
*Single molecule biophysics*
Find all the relevant details on this page
https://www.mosbri.eu/training/basic-level-schools/bls2/

This basic-level school is aimed at biologists, biophysicists, biochemists,
structural biologists, etc., who want to learn a technique enabling high
throughput screening for dynamic parameters of biochemical interactions on
a single molecule level.

The deadline for submission of an application to participate in this course
is:  *31 March 2024*.

*Invited speakers*
Carsten Janke, Institut Curie
Tim Mitchison, Harvard Medical School

*There is no participation fee. There are twenty travel bursaries of a
maximum 200 euros to cover travel costs and local accommodation in shared
twin hotel rooms. *

Apply via the course web page
*https://www.mosbri.eu/training/basic-level-schools/bls2/
*
or contact directly the course organizers for more information
zdenek.lan...@ibt.cas.cz (Scientific Organizer)
magdalena.schneider...@ibt.cas.cz (Course Admin)


Jan Dohnalek
MoB-IBT centre of MOSBRI



-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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[ccp4bb] wwPDB News: CryoEM Archiving and Validation Recommendations

2024-03-14 Thread Deborah Harrus 

Dear all,

A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss 
data requirements for deposition and validation of cryoEM structures, 
with a focus on single-particle analysis and setting community 
recommendations.


The outcomes of this meeting have now been published in this manuscript 
which highlights the recent achievements made by the wwPDB in the space 
of 3DEM validation and the community recommendations going forward.


Some of these recommendations have already been implemented, such as a 
three-tiered strategy powered by the Validation Analysis (VA) pipeline 
for the dissemination of validation information and ensuring the that VA 
can be run by external applications.


   *Community recommendations on cryoEM data archiving and validation*
   Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Cathy Lawson,
   Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf,
   Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard
   Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J.
   Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J.
   Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato,
   Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N.
   Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson,
   Carsten Sachse, Osman Salih, Sjors H.W. Scheres, Gunnar F.
   Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang,
   Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y.
   Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle
   Morris, Ardan Patwardhan, Sameer Velankar
   (2024)/IUCrJ/11: 140–151https://doi.org/10.1107/S2052252524001246

Kind regards,

Deborah Harrus

on behalf of the wwPDB


--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] Open positions for one Postdoc and one PhD student

2024-03-14 Thread Clemens Grimm 
Dear All,

Two research positions funded by the VolkswagenStiftung are available in the 
group of Prof. Utz Fischer at the Theodor-Boveri Institute of the 
Julius-Maximilians-Universität Würzburg.

The successful candidates will participate in a structure-based drug design 
approach to combat the zoonotic risk imposed by poxviral reservoirs and human 
pathogenic poxvirus strains. To this end, we target the unique poxviral 
transcription machinery, which relies exclusively on virus-encoded proteins. As 
a basis, we recently reported the isolation and comprehensive structural 
investigation of this machinery in different phases of action. This now enables 
the identification and design of small molecules that interfere with poxviral 
gene expression and their subsequent translation into antiviral 
pharmaceuticals. Last but not least, the unexpected severity of the ongoing 
monkeypox outbreak underlines the timeliness of this project.

See our recent publications on the topic:
Grimm et al., Cell 179 (7): 1537-1550 (2019)
Hillen et al., Cell 179 (7): 1525-1536 (2019)
Grimm et al., Nat. Struct. Mol. Biol. 28 (10), 779-788 (2021)
Grimm et al., TIBS (2022)

or for a quick overview our website:
https://www.biozentrum.uni-wuerzburg.de/biochem/research-groups/grimm-group-structural-biology/projects/

We offer:
A stimulating international research environment in a well-equipped and modern 
department at the Biocenter of the University, which provides diverse 
opportunities for collaborations. The GSLS provides the framework for a 
structured PhD education program. Remuneration will be according to public 
service positions in Germany, 100% TV-L E13 (Postdoc) or 65% TV-L E13 (PhD 
student). Disabled applicants will be preferentially considered in case of 
equivalent qualifications.

Requirements:
The candidates should possess a solid background in biochemistry or virology. 
The Postdoc position requires a PhD in the life sciences. The PhD Student 
position requires an M.Sc. in the life sciences or equivalent for enrolment at 
the Würzburg Graduate School of Life Sciences (GSLS). Experience in protein 
bioinformatics, biophysics or structural biology is beneficial.

Application/ Contact:
Please send your application, which should include a statement of motivation, a 
detailed CV and the contact details of two referees as a single file by e-mail 
to the Department of Biochemistry.

For further information, please contact
Utz Fischer utz.fisc...@uni-wuerzburg.de   Tel.: +49 
931-3184029 or
Clemens Grimm clemens.gr...@uni-wuerzburg.de   Tel.: +49 931-3184031




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[ccp4bb] New, free online AlphaFold training course

2024-03-14 Thread Deborah Harrus 

Dear all,

Recognising the transformative impact of AlphaFold on scientific 
research, EMBL-EBI and Google DeepMind have co-developed a comprehensive 
online training course to facilitate the wider adoption and responsible 
use of this technology.


The training course, launched last week offers an interactive learning 
experience tailored to different levels of expertise. It enables users 
to delve into the fundamentals of AlphaFold, explore its strengths and 
limitations, and gain practical skills through hands-on exercises.


The AlphaFold training course is now available on the EMBL-EBI Training 
platform: https://www.ebi.ac.uk/training/online/courses/alphafold/


If you have any questions about the course, please reach out to the 
EMBL-EBI training team on trainonl...@ebi.ac.uk.


Kind regards,

Deborah Harrus

PDBe

--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] Postdoc position in the XFEL Hub at Diamond Light Source

2024-03-14 Thread Orville, Allen (DLSLtd,RAL,LSCI) 
Hi,

The XFEL Hub at Diamond Light Source in Oxfordshire UK, has a Postdoctoral 
Research Associate position open (three years duration) to address 
time-resolved, dynamic structural biology. We are eager to work with you on 
serial crystallography correlated with X-ray emission spectroscopy with 
applications and data collected at Diamond and at XFELs, including SwissFEL.

More information and the application process are in the link below.
https://vacancies.diamond.ac.uk/vacancy/postdoctoral-research-associate-xfel-hub-552310.html

The initial closing date for applications is 02 April 2024, however 
applications will be reviewed and interviewed on an ongoing basis until this 
vacancy is filled.

AMO
~ ~ ~ ~ ~
Allen M. Orville, Ph.D.
Wellcome Investigator
Principal Scientist, XFEL Hub at Diamond Light Source
Harwell Science and Innovation Campus
Didcot, Oxfordshire
OX11 0DE
United Kingdom

Phone: +44 (0) 1235 567505
Mobile: +44 (0) 7471 026061
email: allen.orvi...@diamond.ac.uk

AMO site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub/Staff/Orville.html
XFEL-Hub site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub.html






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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-14 Thread Navdeep Sidhu 

Dear Fred,

I hope you'd agree that another good way to bypass similar issues is 
that before working on data where you don't know the model, you try out 
data where you do. And so I'd recommend this book, which provides you 
with practice data and great worked tutorials:


Peter Müller (Ed.). Crystal Structure Refinement: A Crystallographer's 
Guide to SHELXL.  IUCr/Oxford, 2006 
.


The book uses XP for visualization (which I guess some people still use) 
but, as Tim suggested, you should certainly also try out ShelXle or 
Olex2. (I think it's fair to say that we couldn't have identified some 
density issues just using XP.)


(A 2nd edition of the book would also be a great idea.)

Best regards,
Navdeep

---
Navdeep Sidhu
Germany
Web: https://scholar.google.de/citations?user=ZqU1AE0J&hl=de
---


---
On 12.03.24 16:42, Frederic Vellieux wrote:

Hi,

In fact the problem was solved with the help of Ivica Dilovic from 
Zagreb who suggested some changes to the shelxl .ins file. After these 
modifications the cryptic error message was still there, but the 
modifications made me try to remove one card. That did it.


So the part that is concerned with this error in the .ins file is as 
follows:


did not work and gave the cryptic error message:
TITL 240223Ru_complex_0m_5 in P1
CELL 1.34139  10.36240  11.17780  13.19300  80.8589  73.7519  71.3166
ZERR    2.00   0.00070   0.00080   0.00090   0.0026   0.0023   0.0023
LATT -1
SFAC C H N O CL RU
UNIT 62 64 2 10 2 2
TEMP -163.150
TREF
L.S. 10
EXTI 0.001
WGHT 0.0617
BOND $H
CONF
HTAB
FMAP 2
PLAN 20
FVAR 0.75351

worked and gave no error:
TITL 240223Ru_complex_0m_5 in P1
CELL 1.34139 10.3624 11.1778 13.193 80.8589 73.7519 71.3166
ZERR 2 0.0007 0.0008 0.0009 0.0026 0.0023 0.0023
LATT -1
SFAC C H N O Cl Ru
DISP C 0.0137 0.0067 57.1
DISP Cl 0.3281 0.5435 4162.2
DISP H 0 0 0.6
DISP N 0.0241 0.0134 109.9
DISP O 0.0389 0.0241 193.4
DISP Ru -0.076 2.5955 20068.6
UNIT 62 64 2 10 2 2
L.S. 10
PLAN  10
TEMP -163.15
CONF
BOND $H
HTAB
MORE -1
fmap 2
WGHT 0.1
FVAR 0.25491

I guess it would be much better (from the user's point of view) if 
SHELXL would write on the output what the offending line is.


Also, no indications are given on the SHELX site where the Windows .exe 
files are supposed to go. They must be placed in the directory where the 
GUI (olex2 or WingX) stores its exe file (olex2.exe or wingx.exe). I 
just tried to place them there because I was desperate and it worked.


Cheers, and thanks to everyone for their suggestions.

Fred.

On 2024-03-12 16:12, Kay Diederichs wrote:

Fred,

nobody would be offended if you'd just post your SHELXL .ins file 
here; there are enough experienced crystallographers to spot the mistake.
Best would be if you could pare it down to small size, but such that 
it is still reproducible (my own experience is that this almost always 
makes me find my own mistakes).


But to try and answer your title question, there is the 
bruker-...@g-groups.wisc.edu mailing list.


Best wishes,
Kay



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[ccp4bb] isymop reference for ISYM column in MTZ files

2024-03-14 Thread Hekstra, Doeke Romke 
Hi,

I would like to be sure about which symmetry operation the M/ISYM column in an 
MTZ file is referring to. Is it correct that this matches the order in CCP4's 
/lib/data/syminfo.lib (at least when this order is unique-it is not always so)? 
Would anyone know why the order in one of my favorite websites 
(http://img.chem.ucl.ac.uk/sgp/large/sgp.htm) happens to often be different?

Thank you,
Doeke

=

Doeke Hekstra
Assistant Professor of Molecular & Cellular Biology, and of Applied Physics 
(SEAS),
Director of Undergraduate Studies, Chemical and Physical Biology
Center for Systems Biology, Harvard University
52 Oxford Street, NW311
Cambridge, MA 02138
Office:617-496-4740
Admin:   617-495-5651 (Lin Song)





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