[ccp4bb] Reminder: CBMS Lecture Series - May 18, 2022; 13:30 - Michael Ragusa, Dartmouth College

[Stojanoff, Vivian]

Please join us for ……



Michael Ragusa

Dartmouth College



WEDNESDAY, May 18, 13:30 (EDT)



"Two Stories of Degradation – Investigating the Initiation of Selective 
Autophagy in Yeast"



Register in advance for this meeting:


 https://bnl.zoomgov.com/meeting/register/vJIsde6ppjIqGCTAbMCARjdtKas5xKciYEg



San Francisco 10:30 - NYC 13:30 -  London 18:30 - Paris 19:30 - Mumbai 23:00 - 
Tokio 2:30 (May 19) - Sidney 3:30 (May 19)



Abstract:

Autophagy is a cellular degradation process in which cytosolic material is 
captured in double membrane vesicles and targeted to lysosomes in mammalian 
cells or the vacuole in yeast for degradation. One cargo that can be degraded 
by autophagy is mitochondria. The degradation of mitochondria by autophagy 
requires the organization of many soluble proteins on the surface of 
mitochondria to generate distinct initiation sites for this process. We have 
been utilizing a combination of biochemistry, cell biology and structural 
biology to investigate how these initiation sites are organized and how these 
initiation sites recruit membrane.





[cid:4bbce247-f69d-4c92-837f-5dabeb00c441]



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[ccp4bb] PhD scholarship at the IBS in Grenoble, France

[Antoine Royant]

Dear colleagues,

There is a PhD student position available in my team on the 
structure-based development of novel infrared fluorescent proteins. We 
plan to use AlphaFold, X-ray crystallography and various biophysical 
techniques in the project.


https://www.labex-gral.fr/wp-content/uploads/2022/03/InfrafredFP800-1.pdf

Best regards,

Antoine.

--
Antoine ROYANT
Institut de Biologie Structurale
71 avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9
FRANCE
Phone +33(0)4-76-88-17-46 or +33(0)-4-57-42-85-39
antoine.roy...@esrf.fr or antoine.roy...@ibs.fr



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[ccp4bb] AICS2022 International School of Crystallography - "Protein structure models, biophysical data and high-performance computing for drug design" – BOOK THE DATE – first announcement

[MICHELE CIANCI]

Dear Colleagues,

Registration will be open soon for the AIC School:
"Protein structure models, biophysical data and high-performance computing for 
drug design"

The AICS2022 school focuses on the exploitation of protein structures, from 
crystallography, electron microscopy and AI as well as biophysical data and 
computer simulations, for drug discovery.
The aim of the school is to introduce young researchers from chemistry, 
structural biology, biophysics and biochemistry to the latest developments in 
the field, and to provide a theoretical and practical overview of 
state-of-the-art tools in structure-based drug design, using both computational 
(docking, virtual screening and molecular dynamics) and biophysical techniques.

The speaker line-up includes:

Silvia Onesti, Elettra Synchrotron, Trieste (IT),
Chair of the School

Manfred Weiss, Helmhotz-Zentrum Berlin (DE)
Maria Letizia Barreca, University of Perugia (IT)
Rob Nicholls, MRC Lab of Molecular Biology (UK)
Anna Marabotti, University of Salerno (IT)
Roberto Steiner, King’s College London (UK), University of Padova (IT)
Adriana Pietropaolo, University of Catanzaro (IT)
Alessandra Magistrato, CNR-IOM c/o SISSA (IT)
Mattia Sturlese, University of Padova (IT)
Giuseppe Felice Mangiatordi, Institute of Crystallography-CNR (IT)
Andrea Astolfi, University of Perugia (IT)
Angelo Spinello, University of Palermo (IT)
Luigi Scietti, IEO Research (IT)
Benny Danilo Belviso, Institute of Crystallography-CNR (IT)
Michele Cianci, Marche Polytechnic University (IT)
Federico Forneris, University of Pavia (IT)
Menico Rizzi, University of Eastern Piedmont (IT)

The school will be held in presence from the 7th till the 10th of September 
2022 at the University of Trieste (Italy).
For more information, program and registration details please visit:

https://school2022.cristallografia.org/

We look forward to hosting you at the school in September.

Kind regards,

Michele Cianci
Elisa Boanini
Danilo Belviso
Paolo Pio Mazzeo

 the Italian Crystallographic Association (AIC) Commission for Crystallography 
Teaching



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[ccp4bb] H atoms in refined structure

[Luca Mazzei]

Dear CCP4 people,

Refining a 1.7 Angstroem structure with REFMAC (CCP4i2) using hydrogens during 
refinements by generating riding hydrogens I obtain a PDB file that does not 
contain H atoms. However, the corresponding mmcif file that I should use for 
deposition contains their coordinates and give them either full or zero 
occupancy. Do you know how I can safely delete H atoms from the mmcif file 
prior deposition? Would this affect Rwork and Rfree calculated upon validation 
on the wwPDB?

Thanks in advance,

Luca Mazzei


Luca Mazzei - PhD
Laboratory of Bioinorganic Chemistry
Department of Pharmacy and Biotechnology (FaBiT)
Alma Mater Studiorum - University of Bologna
Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
Tel: +39 0512096235







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[ccp4bb] Exciting post-doc position available on DNA transcription and conjugation at the ALBA synchrotron

[Roeland Boer]

Dear fellow structural biologists,

I would appreciate it if you could forward this message to anyone that 
might be interested.


We are looking for an enthusiastic and motivated early-career postdoc to 
study the structural aspects of auxin-dependent transcription regulation 
in plants, and/or plasmid conjugation in gram-positive bacteria at the 
ALBA synchrotron (Barcelona, Spain).


The project is a continuation of the research lines of a highly 
successful research group, including publications in Cell 
(10.1016/j.cell.2013.12.027), Nature Communications 
(10.1038/s41467-020-16032-y), Nucleic Acids Research 
(10.1093/nar/gkaa540 and 10.1093/nar/gky996), Nature Plants 
(10.1038/s41477-020-0662-y) and PNAS (10.1073/pnas.2009554117).


At the ALBA synchrotron, exciting times lie ahead for structural 
biologists. Recently, a new EM facility has been built and is being 
commissioned at the moment. In addition, an upgrade of the storage ring 
will come to fruition in the coming 5-10 years. Furthermore, a 
microfocus beamline is under construction that will be open to friendly 
users in the year to come. These instruments will complement the 
macromolecular crystallography, SAXS, infrared microscopy and X-ray 
microscopy beamlines currently in operation. The facility is located 
near Barcelona, which is a great city to live and work.


For inquiries, please contact me at rb...@cells.es. To apply, please 
check the following page:


https://public.cells.es/jobs/#!/jobs/postdoctoral-researcher-position-mineco-research-grant-pid2020-117028gb-i00

Best,

Roeland.
--



Roeland Boer
XALOC beamline- Experiments Division
ALBA SYNCHROTRON LIGHT SOURCE
Carrer de la Llum 2-26 | 08290 | Cerdanyola del Vallès| Barcelona | 
Spain 

(+34) 93 592 4333
www.albasynchrotron.es | rb...@cells.es 
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Re: [ccp4bb] To print the results of CCP4 CONTACT

[Rafiga Masmaliyeva]

Thank You all for your answers.

Best, Rafiga

On Wed, May 11, 2022 at 5:53 PM Jon Cooper 
wrote:

> Hello, something like:
>
> ccp4prog xyzin input.pdb > output.log
>
> Or:
>
> ccp4prog xyzin input.pdb > & output.log
>
> if output.log already exists.
>
> HTH, Jon.C.
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 11 May 2022, 15:48, Rafiga Masmaliyeva < rmasmaliy...@gmail.com> wrote:
>
>
> Hi.
>
> I run CCP4 CONTACT with command line.
> Which command do I need to add to be able to print the results to a text
> file if it is possible?
>
> Thank you in advance.
>
> Best regards
> Rafiga
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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>

-- 
Rafiga Masmaliyeva, PhD
University of Hamburg
Department of Chemistry
Institute of Physical Chemistry
Grindelallee 117
D-20146 Hamburg
Germany

phone: +49 40428383257
web:
https://www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck/personen.html



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[ccp4bb] today's abstracts deadline; 33rd European Crystallographic Meeting

[Orville, Allen (DLSLtd,RAL,LSCI)]

Hi,

This is a reminder that today is the deadline for abstracts to the 33rd 
European Crystallographic Meeting. The meeting will be held at the recently 
refurbished Music Conservatory and Congress Centre in Versailles, close to 
Paris, between 23rd and 27th of August 2022.

Jean-Paul Itié, Sylvain Ravy and Andrew Thompson (for the organizing committee)
https://www.ecm33.fr/

I’ll add that Prof Ilme Schlichting and I are organising the “MS6 - Structural 
Enzymology” session to be held on Thursday, 25.Aug.2022

Sincerely,

AMO
~ ~ ~ ~ ~
Allen M. Orville, Ph.D.
Wellcome Investigator and Royal Society Wolfson Fellow
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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