[ccp4bb] PhD student position in Finland

[Lari Lehtiö]

Dear colleagues,


We have a 4-year PhD student position for 2020-2023 open in my team. The 
project focuses on structural and functional characterization of human 
ADP-ribosyltransferases.


For more details and application form please see the web application portal:

https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=7633=en


Note that applications received by email will not be considered.


Best regards,


Lari



__
Lari Lehtiö, Professor
Faculty of Biochemistry and Molecular Medicine
P.O.Box 5400
FIN-90014 University of Oulu
Finland
http://www.oulu.fi/biocenter/groups/lehtio
_



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Re: [ccp4bb] Refinement of Occupancy in Refmac

[Christian Roth]

Hi Deniz,
yes you can do that, though I don't know right now how B-factors are taken
into account when refining occupancies.
Anyway, in i2 you have to go to the advanced tab. There is a  place to put
keywords in (text area). There you put the right combination of keywords
for your special cases. Regarding syntax, please look here.

http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#Occupancy

Hope you find the right combination of keywords and it will work out for you

Cheers

Christian

On Mon, Jun 24, 2019 at 10:57 PM "Deniz Üresin" 
wrote:

> Hello,
> when I add an alternative conformation of a residue in COOT, I have to set
> the occupancy of both conformers, but Refmac5 won't touch these numbers.
> Can I tell Refmac to check for the best fitting occupancies (in the Windows
> version of CCP4i2)?
>
> With kind regards,
> Deniz Üresin
>
> Institute for Biophysics
> Goethe-University Frankfurt
> Max-von-Laue-Straße 1
> 60438 Frankfurt/Main
>
> --
>
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[ccp4bb] Refinement of Occupancy in Refmac

[Deniz Üresin]

Hello,

when I add an alternative conformation of a residue in COOT, I have to set the occupancy of both conformers, but Refmac5 won't touch these numbers. Can I tell Refmac to check for the best fitting occupancies (in the Windows version of CCP4i2)?

With kind regards,
Deniz Üresin

Institute for Biophysics
Goethe-University Frankfurt
Max-von-Laue-Straße 1
60438 Frankfurt/Main


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[ccp4bb] Beamline Scientist position on PROXIMA 2A

[SHEPARD William]

Hi Everybody, 

Just as a reminder, we recruiting a Beamline Scientist (permanent position) on 
PROXIMA 2A at Synchrotron SOLEIL, which would be an excellent opportunity for a 
suitably motivated scientist.

Please refer to the link below for more information:

https://www.synchrotron-soleil.fr/en/job-offers/scientist-proxima-2a-beamline-mf

Kind regards, 
Bill

William SHEPARD
PROXIMA 2A 
Synchrotron SOLEIL
Gif-sur-Yvette
France

email: william.shep...@synchrotron-soleil.fr


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Re: [ccp4bb] different residues as alternate occupancy?

[Georg Mlynek]

Dear Guenter, yes look at crambin (pdbcode 1EJG).


This crashes Coot until you add*

  allow_duplicate_sequence_numbers()

to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these can be found (added to) the
directory in which Coot was installed (e.g. C:\WinCoot).

To resolve your problem look at

https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12

example 5

Br, Georg.


Am 2019-06-24 um 4:22 PM schrieb Savvas Savvides:
The structure of milk proteins obtained from in vivo-grown crystals 
from a viviparous cockroach could also serve as an interesting case:


http://dx.doi.org/10.1107/S2052252516008903

best wishes
Savvas


On 24 Jun 2019, at 16:03, Holton, James M 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk 
> wrote:


A classic case of this is crambin.  Residue 25 of 3nir.

-James Holton
MAD Scientist

On 6/24/2019 1:00 AM, Guenter Fritz wrote:

Dear all,

I am refining a multimer and mass spec data of the sample indicate
that there is a mixture of two variants which differ in one amino acid
residue. The density that we see is therefore most likely an average
of both variants. I have created a pdb file with "alternate residues"
each with 0.5 occupancy at this position to use it in refinement.
However, the programs detect this as an error in the pdb file.

Has anyone  faced such a problem previously? Any suggestions are very
much appreciated.

Thanks a lot and best regards, Guenter



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Re: [ccp4bb] different residues as alternate occupancy?

[Savvas Savvides]

The structure of milk proteins obtained from in vivo-grown crystals from a 
viviparous cockroach could also serve as an interesting case:

http://dx.doi.org/10.1107/S2052252516008903 


best wishes
Savvas


> On 24 Jun 2019, at 16:03, Holton, James M 
> <270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> A classic case of this is crambin.  Residue 25 of 3nir.
> 
> -James Holton
> MAD Scientist
> 
> On 6/24/2019 1:00 AM, Guenter Fritz wrote:
>> Dear all,
>> 
>> I am refining a multimer and mass spec data of the sample indicate 
>> that there is a mixture of two variants which differ in one amino acid 
>> residue. The density that we see is therefore most likely an average 
>> of both variants. I have created a pdb file with "alternate residues" 
>> each with 0.5 occupancy at this position to use it in refinement.  
>> However, the programs detect this as an error in the pdb file.
>> 
>> Has anyone  faced such a problem previously? Any suggestions are very 
>> much appreciated.
>> 
>> Thanks a lot and best regards, Guenter
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 
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[ccp4bb] 3rd International Meeting of HeCrA's young researchers

[E. Kyriakis]

Dear all,



We invite young scientists to participate at the 3rd International Meeting
of HeCrA (Hellenic Crystallographic Association) for young researchers that
will be held on 13-14 July, 2019 at the University of Patras in Patras,
Greece.

The meeting aims to reinforce European scientific communication and
speakers will emphasize on the methodology, difficulties as well as
troubleshooting steps they followed during their research. The event is
supported by the European Crystallographic Association (ECA).

10 scholarships of 100 euros will be available for young participants from
abroad. To apply for the scholarship, please, send a short CV and apply at
our email address (hecra.jun...@gmail.com).



For more details please visit our website:
https://sites.google.com/view/hecra/hecra-young-researchers



Abstract submission deadline: 30/6/2019



Looking forward to seeing you in Patras,



On behalf of the organizing committee

-- 
Efthimios Kyriakis
Department of Biochemistry & Biotechnology
University of Thessaly, Biopolis, 41500, Larissa
(+30) 2410565297



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Re: [ccp4bb] different residues as alternate occupancy?

[Holton, James M]

A classic case of this is crambin.  Residue 25 of 3nir.

-James Holton
MAD Scientist

On 6/24/2019 1:00 AM, Guenter Fritz wrote:
> Dear all,
>
> I am refining a multimer and mass spec data of the sample indicate 
> that there is a mixture of two variants which differ in one amino acid 
> residue. The density that we see is therefore most likely an average 
> of both variants. I have created a pdb file with "alternate residues" 
> each with 0.5 occupancy at this position to use it in refinement.  
> However, the programs detect this as an error in the pdb file.
>
> Has anyone  faced such a problem previously? Any suggestions are very 
> much appreciated.
>
> Thanks a lot and best regards, Guenter
>
> 
>
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[ccp4bb] Postdoc vacancy in cryo-EM of Gene Regulatory Complexes at Schalch Lab, University of Leicester

[Schalch, Thomas (Dr.)]

Dear all,

Our position for a postdoc in structural biology is still open! Please spread 
the word or apply until 28th June, 2019 for an exciting challenge to study gene 
regulatory complexes. Great opportunity for hands-on cryo-EM at the Leicester 
Institute of Structural and Chemical Biology. https://go.nature.com/2WQLErZ

Thank you,

Thomas


From: Schalch, Thomas (Dr.)
Sent: Tuesday, May 28, 2019 9:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Postdoc vacancy in cryo-EM of Gene Regulatory Complexes at Schalch 
Lab, University of Leicester

Dear all,

A postdoctoral position is available in structural biology at the Leicester 
Institute of Structural and Chemical Biology, Department of Molecular and Cell 
Biology, University of Leicester.

We have an exciting opportunity for highly motivated postdoctoral candidates to 
lead a new project, which tackles fundamental questions in the regulation of 
gene expression through chromatin modification. The post of Research Associate 
is funded by the BBSRC to investigate the role of H2B ubiquitylation in 
heterochromatin formation and its mechanism in the promotion of euchromatic 
domains. The Research Associate will join a vibrant community at the University 
of Leicester’s Department of Molecular and Cell Biology and will be based in 
the research group of Dr. Thomas Schalch, which has a long-standing interest in 
structural and functional understanding of chromatin and its impact on gene 
expression.

The Leicester Institute for Structural and Chemical Biology (LISCB) is a centre 
of research excellence initiated by the University of Leicester, which provides 
access to state-of-the-art integrated structural approaches comprising 
cryo-electron microscopy (Titan Krios G3), X-ray crystallography and 
biomolecular NMR.

For informal enquiries please contact Thomas Schalch directly by email at 
thomas.scha...@le.ac.uk.

Information on the application process and further details are available at 
https://jobs.le.ac.uk/vacancies/vacancy-details.aspx?VacancyID=1162.

--
Thomas Schalch, PhD
Associate Professor

Leicester Institute of Structural & Chemical Biology
Department of Molecular and Cell Biology
Henry Wellcome Building
University of Leicester
Lancaster Road, Leicester, LE1 7RH
United Kingdom

t: +44 116 229 7120
e: thomas.scha...@le.ac.uk
w: https://www.schalchlab.org




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[ccp4bb] different residues as alternate occupancy?

[Guenter Fritz]

Dear all,

I am refining a multimer and mass spec data of the sample indicate that 
there is a mixture of two variants which differ in one amino acid 
residue. The density that we see is therefore most likely an average of 
both variants. I have created a pdb file with "alternate residues" each 
with 0.5 occupancy at this position to use it in refinement.  However, 
the programs detect this as an error in the pdb file.


Has anyone  faced such a problem previously? Any suggestions are very 
much appreciated.


Thanks a lot and best regards, Guenter



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[ccp4bb] PhD position at IOCB, Prague

[zoll]

PhD Position in Structural Parasitology at IOCB, Prague

Job description

A PhD position is open in Dr Sebastian Zoll‘s structural biology group at the 
Institute of Organic Chemistry and Biochemistry (IOCB) in Prague. The group is 
interested in understanding the structural basis of interaction between surface 
proteins of eukaryotic parasites and human host factors to provide a foundation 
for the development of novel therapeutic strategies against neglected tropical 
diseases. The successful candidate will be using an integrated structural 
biology approach including X-ray crystallography, small angle X-ray scattering 
as well as single particle Cryo-EM together with a wide range of biophysical 
techniques for characterisation of protein-protein/ligand interactions. The 
position will also include training in the growing field of recombinant 
antibody and nanobody technology which the candidate will be applying in 
structural studies as well as in the development of therapeutics. The project 
is supported by a multidisciplinary network of international collaborators and 
provides excellent opportunities to receive additional training in foreign host 
institutions.

The institute and the city

The Institute of Organic Chemistry and Biochemistry (IOCB) in Prague is the 
leading scientific research institution in the Czech Republic providing a 
dynamic, international environment that brings together researchers from 
various fields such as structural biology, molecular biology, medicinal and 
computational chemistry. 

IOCB is situated near the city centre in a vibrating, historical quarter of 
Prague boasting beautiful architecture and a rich array of public amenities 
such as cafés, pubs, parks and grocery stores. Transport links by metro and 
tram are excellent with short distances to both airport as well as old town and 
Letna park with its stunning views over the Vltava river. 

Due to its long-standing history in applied science and strong ties with the 
pharmaceutical industry, IOCB enjoys an excellent funding situation and offers 
access to facilities for all modern structural and biophysical methods. 
Bacterial and eukaryotic protein expression platforms are available as well as 
Mass Spectrometry and NMR facilities and a computing cluster for data 
processing, structure determination and Rosetta-based protein modelling. A 
state-of-the-art crystallisation facility contains robotics for 96-well-plate 
crystallisation and liquid handling, a Rigaku imaging hotel and an X-ray 
generator equipped with a Pilatus 300K detector. For high-resolution data 
collection there are also regular trips to European synchrotrons. Furthermore, 
a 200 keV cryo-electron microscope will become operational within the next 2 
years at IOCB. In the meanwhile IOCB researchers enjoy privileged access to the 
EM facilities (screening microscopes and Titan Krios) at CEITEC. 

Requirements 

We are looking for candidates with an M.Sc. in biology, biochemistry or a 
related discipline and a strong interest in structural biology. The successful 
candidate must be willing to work as part of a team and have the motivation and 
commitment to design experiments and interpret results independently. 
Experience in structural biology techniques is not required but familiarity 
with recombinant protein expression and protein purification will be a plus. 
Good oral and written communication skills in English are a prerequisite.

How to apply?

Please send a short motivation statement (max. 500 words), a copy of your 
research thesis and M.Sc. certificate, a copy of your CV and contact 
information for two references to sebastian.z...@uochb.cas.cz

Feel free to contact Sebastian for informal enquiries.

Dr Sebastian Zoll
Junior Group Leader
Institute of Organic Chemistry and Biochemistry
Czech Academy of Sciences
Flemingovo namesti 542/2, 166 10 Prague 6
Czech Republic
Phone: +420 220 183 591
Email: sebastian.z...@uochb.cas.cz
Facebook: https://www.facebook.com/IOCBPrague

Recent relevant publications:

Zoll S, Lane-Serff H, Mehmood S, Schneider J, Robinson CV, Carrington M, 
Higgins MK (2018) The structure of serum resistance-associated protein and its 
implications for human African trypanosomiasis. Nature Microbiology 3: 295-301


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