[ccp4bb] 2nd CCP4/BGU Workshop on Advanced Methods for Macromolecular Structure Determination

[Anat Shahar]

Dear all,

We would like to update you that a few places are still available for the 2nd 
CCP4/BGU Workshop on Advanced Methods for Macromolecular Structure 
Determination, which will take place at Ben-Gurion University of the Negev 
(BGU) in Beer-Sheva, Israel, between 23rd February to 4th March, 2020.

The workshop is limited to 25 participants, and everybody who is interested is 
welcome to apply.

The workshop program will be suitable for last-year PhD students, as well as 
postdoctoral researchers and young scientists in their first years of research.

The workshop will embrace the full course of Macromolecular Crystallography and 
Cryo-EM: from data collection to structure solution and PDB Deposition, with a 
particular emphasis on practical aspects of each and every step.
In addition, all participants will have an opportunity to carry out remote data 
collection at Diamond Light Source on their own samples.
A team of leading structural biology software developers from around the world 
will present lectures and tutorials and will also be available to help 
participants with their own projects, such as processing own data and solving 
structures during hands-on sessions of the workshop.
More information, including “how to apply”, registration form and tentative 
program, can be found at: https://lifeserv.bgu.ac.il/wp/ccp4workshop/
The closing date for application is 20.12.2019.
Best wishes,
Anat Shahar & Eugene Krissinel

[cid:image001.jpg@01D1253D.4AF7ED90]
Anat Shahar, PhD
Macromolecular Crystallography Research Center (MCRC)
The National Institute for Biotechnology in the Negev Ltd.
Ben-Gurion University of the Negev
Beer-Sheva, Israel
Tel: +972-8-6461807
Fax: +972-8-6472970
Web: www.bgu.ac.il/crystallography







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[ccp4bb] PDRA: Cheminformatics vacancy at Diamond (von Delft)

[Skyner, Rachael (DLSLtd,RAL,LSCI)]

Hi All,



We are currently advertising a PDRA (cheminformatics) position at Diamond, with 
a focus on developing and implementing new algorithms to combine 
high-throughput natural-product discovery with rapid chemical progression of 
fragment compounds.



The position is funded by CHNUK2. CHNUK2, a collaboration between world-leading 
institutions in the UK and China, aims to form a hub of support platforms for 
fundamental and translational antibiotic discovery research. Using UK strengths 
in underpinning biology and science policy, the project aims to explore and 
exploit China’s resources in natural products and traditional Chinese medicine.



The deadline for applications is 02/01/2020. Could you please circulate the ad 
to any parties who may be interested in the position?



https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-chemoinformatics-406236.html



Thanks in advance,

Dr. Rachael Skyner
PDRA (XChem)

Diamond Light Source Ltd.
Diamond House, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE

Tel:  +44(0)1235 56 7537
Mobile: +44(0)7540 95 5786 (Out of office)

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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] Open position at EMBL Grenoble - Scientific Expert for Eukaryotic Protein Production

[Marco Marcia]

Dear all
a kind reminder about the open position advertised below.
Regards
Marco

On 12/11/2019 09:46, Marco MARCIA wrote:

Dear all
I am writing to let you know that EMBL Grenoble has an opening for a 
Scientific Expert for Eukaryotic Protein Production.

*Closing date: Jan 15th 2020.*
You can read more about the position and submit your application at:
https://www.embl.de/jobs/searchjobs/index.php?ref=GR00141=1

Regards
Marco


--
Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)476207634
phone (office): 0033-(0)476207759
fax: 0033-(0)476207199
email:mmar...@embl.fr
web:https://embl.fr/research/unit/marcia/



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--
_

Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)476207634
phone (office): 0033-(0)476207759
fax: 0033-(0)476207199
email: mmar...@embl.fr
web: https://embl.fr/research/unit/marcia/




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[ccp4bb] Research Vacancies and PhD Studentships - Portsmouth Centre for Enzyme Innovation

[John McGeehan]

Dear Colleagues,


We would like to announce the opening of 7 research posts and 3 PhD
studentships in our new Centre for Enzyme Innovation (CEI
). The CEI has a focus around the development of
biological solutions for plastic recycling and biomass conversion. If you
are interested in joining our growing team in a well supported research and
innovation environment, please see the adverts below.

*Senior Research Fellows*

·Surface Analysis (advert

)

·Molecular Dynamics (advert

)

*Senior Research Associates*

·RNA Synthetic Biology, 2 posts (advert

)

·Bioinformatics (advert

)

*Specialist Technician*

·Microbial culture and sequencing library preparation (advert
)

*Industry Engagement Post*

·Innovation Fellow (advert

)

*PhD Studentships x3* (link

)

·   Designing and evolving plastic-degrading enzymes for new function


·   Exploring the genome architecture of plastic-degrading bacteria


·   Structural and biophysical characterisation of novel plastic
degrading enzymes


The CEI was recently awarded a £5.8m grant from Research England and '*STEM
Research Project of the Year*' by Times Higher Education.

Full job descriptions and person specifications are available on our
recruitment
website  (https://port.engageats.co.uk/).
See ‘External vacancies’. Please note that some of the positions have a
closing date in early January. Thank you for your interest.


Best Regards,

John
-- 
*Professor John McGeehan*
--
Director, Centre for Enzyme Innovation (web
),
Institute of Biological and Biomedical Sciences (web
),
School of Biological Sciences,
University of Portsmouth,
King Henry Building,
PO1 2DY, UK
--
Email: john.mcgee...@port.ac.uk
Tel:+44 (0) 2392 842042
*PA: Jacky Dillon *
Email: jacky.dil...@port.ac.uk
Tel: +44 (0) 23 92842023

- *An interview with the BBSRC, 2019*  -



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[ccp4bb] PhD / PostDoc positions @NKI Amsterdam

[Anastassis Perrakis]

Dear all,

We are looking for enthusiastic, motivated PhD students and Post-Docsto join 
the Division of Biochemistry in the Netherlands Cancer Institute 
(https://www.nki.nl) in the groups of Tassos Perrakis and Titia Sixma. If you 
have a keen interest in the general field of integrative structural cell 
biology, and previous experience in cryo-EM, X-ray crystallography, cell 
biology, biochemistry, or biophysics … well, read on!

The project in the laboratory of Titia Sixma 
(https://www.nki.nl/divisions/biochemistry/sixma-t-group/ ) is in the area of 
DNA repair.

The projects in Anastassis (Tassos) Perrakis group 
(https://www.nki.nl/divisions/biochemistry/perrakis-a-group/) are in the 
general field of controlling the progress of cell division and microtubule 
interacting proteins, in lysolipids signaling focusing on Autotaxin and its 
interactions, and together with Robbie Joosten in  PDB-REDO .

The Netherlands Cancer Institute is an international center of excellence with 
a high standard of biological research and outstanding research facilities, and 
has an interactive atmosphere. It is located in Amsterdam, with all its 
cultural amenities, close to the Schiphol airport.

The two groups share a common research infrastructure in the Department of 
Biochemistry, and have an interest in structural studies coupled to functional 
analysis. Facilities include the ability to produce and purify proteins in 
bacterial, insect, and mammalian cells, and a well-equipped macromolecular 
biophysics laboratory that are sites in the Instruct Centre NL 
(https://instruct-eric.eu/centre/protein-facility---nki/).
 Equipment for structural analysis is spearheaded by a brand-new cryo-EM (Jeol 
F2 200kV with a K2 detector) and high-throughput crystallisation robotics; 
these local facilities are coupled with regular access to Krios cryo-EM at 
NeCEN (https://www.necen.nl , https://instruct-eric.eu/centre/necen---lu/) and 
to the ESRF, SLS and DLS synchrotrons, and access possibilities for NMR 
experiments 
(https://instruct-eric.eu/centre/bijvoet-center---uu/).
 Dedicated computing facilities include privileged access to both CPU and GPU 
clusters. Both groups participate in various European and National 
collaborative projects and are members of the Oncode Institute 
(https://www.oncode.nl).

We are looking flexibly for either highly motivated PhD students (strong 
master-level placements in reputable laboratories and familiarity with some of 
the methods we outline would be strong plus) or post-docs (experience in 
cryo-EM would be highly desirable for most positions; candidates with a strong 
background and track record in X-ray crystallography, protein purification, 
cell biology, would be taken seriously under considerations depending on the 
project). For the PDB-REDO project a background in bioinformatics and some 
experience in computerprogramming would be necessary. Applicants should write 
an email, stating their specific interests and attaching a CV and names of 
three references to t.sixma.AT.nki.nl or 
a.perrakis.AT.nki.nl; feel free to also make 
informal inquiries.

We expect applications to be sent in by Monday 13th January and all positions 
are available asap. PhD candidate positions are for four years; post-doc 
positions can be for 1-4 years depending on qualifications and experience; the 
CAO salary levels apply according to the NKI collective agreement.


Anastassis Perrakis and Titia K. Sixma







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[ccp4bb] PhD position in time-resolved protein crystallography

[Padeste Celestino (PSI)]

The Swiss Nanoscience Institute (SNI) is funding a 
PhD Project of the Paul Scherrer Institute in 
collaboration with Prof. Thomas R. Ward 
 at University of Basel, which 
combines method development in serial crystallography at SwissFEL and SLS with 
fundamental science on protein binding.

For this highly interdisciplinary project, we are seeking for a PhD student 
holding a master's degree in science or engineering, with experience in protein 
crystallography, nanofabrication technology and/or peptide synthesis, and with 
keen interest in method development for experiments at state-of-the art large 
scale facilities in order to address fundamental biochemical questions.

Information for applicants for the PhD position is found on the Webpage of the 
SNI PhD School, project number 
1904.

Thanks for spreading this information to potential PhD students.

Kind Regards

Celestino Padeste
__
Paul Scherrer Institut
Dr. Celestino Padeste
ODRA/105
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

Telefon: +41 56 310 21 41
E-Mail: celestino.pade...@psi.ch



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

[Randy Read]

Dear Jessica,

Good to hear that you've solved it!

We're currently putting a lot of work into making the tNCS treatment in Phaser 
more robust.  Would it be possible to share more information about your case so 
we can understand why it was necessary to manually turn off tNCS in that case?  
Having the data (which we would only use for this purpose) would be best, if 
you could send that off-line.  If you don't feel able to share the data, then 
sample log files from an unsuccessful run and the eventual successful run might 
give us some hints.

Best wishes,

Randy Read

> On 16 Dec 2019, at 21:29, Jessica Besaw  wrote:
> 
> THE PROBLEM IS SOLVED! 
> 
> Thank you all for you suggestions. I applied all the suggestion across all 
> datasets collected (not just the one shown above).
> 
> The error & solution: Incorrect space group assignment (new space group P 21 
> 2 21) and ignoring tNCS. 
> 
> This is the BEST Christmas gift a crystallographer could get.  Thank you 
> everyone!
> 
> Cheers!
> 
> Jessica 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Mon, 16 Dec 2019 at 16:16, Wim Burmeister  > wrote:
> Hello,
> I would guess that the badly fitting molecule may be upside down (related my 
> an 2-fold axis).
> I would use the first, partially refined structure for another round of 
> molecular replacement in P212121 with molrep, using the model as well as a 
> partial solution as as asearch model.
> The translational self peak in the native Patterson may be misleading. I came 
> recently across a similar problem.
> Regards
> Wim
> 
> De: "Jessica Besaw" mailto:jbesaw1...@gmail.com>>
> À: "CCP4BB" mailto:CCP4BB@JISCMAIL.AC.UK>>
> Envoyé: Lundi 16 Décembre 2019 20:29:38
> Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric 
> unit does not fit density
> 
> There have been two potential space groups:
> P212121 - Rfree = 36%
> P21212 - Rfree = 45% 
> 
> Xtriage reports that twinning is unlikely. 
> 
> Cheers!
> 
> Jessica 
> 
> 
> 
> 
> 
> On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch  > wrote:
> What’s your spacegroup ? RWork / RFree?
> Twinning by any chance?
> 
> Jürgen 
> 
> __
> Jürgen Bosch, Ph.D.
> Division of Pediatric Pulmonology and Allergy/Immunology
> Case Western Reserve University
> 2109 Adelbert Rd, BRB 835
> Cleveland, OH 44106
> Phone: 216.368.7565
> Fax: 216.368.4223
> https://www.linkedin.com/in/jubosch/ 
> 
> CEO & Co-Founder at InterRayBio, LLC
> 
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> 
> On Dec 16, 2019, at 1:50 PM, Jessica Besaw  > wrote:
> 
> I am crystallizing this membrane protein in a medium (bicelles) that forms 
> lamella like sheets that stack on top of each other. 
> The layer packing is shown below. Is this structure unreasonable?
> 
> 
> 
> On Mon, 16 Dec 2019 at 13:38, Reza Khayat  > wrote:
> Hi Jessica,
> 
> 
> 
> The gap between the two proteins is a bit troubling. Perhaps it's the image, 
> but why would a crystal form if there is no crystal contact between the two 
> proteins?
> 
> 
> 
> Reza
> 
> 
> 
> Reza Khayat, PhD
> Assistant Professor 
> City College of New York
> Department of Chemistry
> New York, NY 10031
> From: CCP4 bulletin board  > on behalf of Ashish Kumar 
> mailto:mail2ashish...@gmail.com>>
> Sent: Monday, December 16, 2019 1:24 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does 
> not fit density
>  
> Hi Jessica,
> 
> It may be possible because of wrong MR solution as well. How were your stats 
> after MR. 
> Also it is correct that it could be possible because of wrong space group.
> Try changing the Space group and repeat MR.
> 
> Best Regards
> Ashish
> 
> On 16 Dec 2019 22:56, "Jessica Besaw"  > wrote:
> Dear community, 
> 
> I am having a lot of trouble solving a protein structure. I think my problem 
> may caused by incorrectly placed proteins in molecular replacement. I have 
> two proteins in my asymmetric unit. It appears that one protein fits 
> perfectly, and the other one has many errors. (See snapshots below). I have 
> tried deleting the parts of the protein (and even the whole protein) to try 
> and rebuild it in COOT, but it was a bit too difficult for me to solve. 
> 
> I would appreciate any and all suggestions for potential strategies moving 
> forward. 
> 
> Other information: 
> (1) 2.4 Angstrom
> (2) 99% complete
> (3) "Translational NCS may be present at a level that may complicate 
> refinement"
> 
> Cheers!
> 
> Jessica 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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> 

[ccp4bb] Job: (Senior) Scientist - Structure-based Protein Engineer - Lonza - Cambridge UK

[Daphne Truan]

Dear CCP4 community,

We are seeking a highly motivated and skilled (Senior) Scientist with 
experience in Structure-based Protein Engineering and Bioinformatics to join 
Lonza's Applied Protein Services (APS) Bioinformatics team based in Cambridge, 
UK.

Key responsibilities:

- The successful candidate will work on multiple customer projects focusing on 
in silico assessments and computational design of diverse proteins.
- You will gain experience on our proprietary platforms for antibody 
humanisation and deimmunisation, immunogenicity (Epibase) and manufacturability 
risk assessments to enhance the developability of potential biotherapeutics.
- The role involves working with customers ranging from small biotech to big 
pharma.
- Additionally, you will contribute to the development of innovative 
technologies to optimize proteins for the manufacturing processes.

Key requirements:

- PhD or equivalent in Structural Biology, Chemistry, Physics or Bioinformatics 
preferably with experience in industry.
- Highly experienced in protein structural analysis with emphasis on homology 
modeling and protein structure-based design. Strong understanding of molecular 
interactions is essential.
- Familiar with biomolecular simulation techniques, including molecular 
dynamics.
- Experienced working in Linux environment and scripting (knowledge of Python 
is essential; Perl is an advantage).
- Ability to generate high quality reports and promote effective communication 
with the customer.
- Advanced analytical and critical problem-solving skills, combined with 
scientific creativity.
- Interest in continuous improvements of processes by integrating innovative 
solutions.
- Ability to work as a team member, as well as independently with minimal 
supervision.
- Fluency in written and oral English, and strong, written, oral communication 
skills.

https://lonza.wd3.myworkdayjobs.com/Lonza_Careers/job/UK---Cambridge/Senior-Scientist_R18977



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