[ccp4bb] Postdoctoral Position at NIH to Study Structures and Mechanisms of Cellular and Viral Noncoding RNAs and RNPs

[Zhang, Jinwei (NIH/NIDDK) [E]]

A postdoctoral position is available in the Structural Biology of Noncoding 
RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology (LMB), 
NIDDK, in NIH’s vibrant main campus in Bethesda, MD near Washington DC. The lab 
addresses a widening gap between the accelerated discovery and functional 
description of the noncoding transcriptome, and the lack of structural and 
mechanistic understanding of complex noncoding RNAs and RNPs. We seek a new 
member to join our diverse group to study gene-regulatory riboswitches, highly 
structured viral RNAs, long noncoding RNAs and their RNP complexes. See 
https://www-mslmb.niddk.nih.gov/zhang/zhanglab.html for details.

The lab is part of the Earl Stadtman Investigator program for high-risk, 
high-impact research at the NIH intramural program consisting of 1100 labs. The 
lab has dedicated access to complete suites of state-of-the-art equipment in 
structural biology (Mosquito, Dragonfly, Rock Imager, Akta Pures, FSEC, etc., 
and regular synchrotron access for X-ray crystallography; Titan Krios and 
Glacios for single-particle Cryo-EM; SAXS, AFM, NMR, etc), cutting-edge 
biochemistry, biophysics (ITC, DSC, SPR, BLI, AUC, DLS, SEC-MALS, CD, 
fluorescence, thermophoresis, iSCAMS, etc), fermentation, advanced mass spec, 
genomics and sequencing, and proteomics core facilities with hands-on training 
or service by PhD-level staff scientists.

We apply innovative technologies to study RNA and RNP structure, dynamics, and 
interactions, such as rational RNA design and engineering, RNA cryo-EM, XFEL, 
ultrafast SAXS/WAXS, single-molecule fluorescence, crosslinking-mass spec., 
etc. Ongoing projects include structural and mechanistic elucidations of the 
T-box riboswitches in bacteria and Gcn2 kinase in eukaryotes in cellular stress 
responses. A second area addresses how numerous viral and host structured 
noncoding RNAs differentially manipulate immune protein activities such as PKR. 
For details refer to recent publications:

Suddala K.C & Zhang, J. (2019) High-affinity recognition of specific tRNAs by 
an mRNA anticodon-binding groove, Nat. Struct. & Mol. Biol., 26, 1114–1122.

Li S. et al., & Zhang, J. (2019) Structural basis of amino acid surveillance by 
higher-order tRNA-mRNA interactions, Nat. Struct. & Mol. Biol., 26, 1094–1105.

Hood, I.V. et al., & Zhang, J. (2019). Crystal structure of an Adenovirus 
Virus-Associated RNA, Nat. Commun. 10:2871

Incoming fellows are also encouraged to bring your own ideas that you could 
develop into research programs that you can then take to your independent PI 
positions. The NIH, NIDDK, and LMB are committed to the continued education and 
career development of trainees through numerous courses and workshops offered 
by OITE, FAES, and NIDDK.

Requirements: Interested candidates must have received (or be expecting) a 
Ph.D. or M.D. within the past five years in molecular biology, structural 
biology, biochemistry, cell biology, or a related discipline, have excellent 
oral and written communication skills, and be strongly self-motivated to 
participate in and design innovative and rigorous research projects. Prior 
experiences in structural biology are not required.

To apply: Please email a cover letter indicating preferred start date, CV, a 
brief summary of research interests, accomplishments, and career goals, and 
names and contact information for at least three references to: Dr. Jinwei 
Zhang, Email: jinwei.zh...@nih.gov. The NIH is dedicated to building a diverse 
community in its training and employment programs. DHHS/NIH is an Equal 
Opportunity Employer. Dec, 20, 2019.

Thank you,
-Jinwei
-
Jinwei Zhang
Laboratory of Molecular Biology
NIDDK, NIH
50 South Drive, Room 4503
Bethesda, MD 20892
Tel: 301-402-4703
https://www-mslmb.niddk.nih.gov/zhang/zhanglab.html





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Re: [ccp4bb] Potential weak binding ligand in the active site

[Barone, Matthias]

Hi Katherine

I'm regularly struggling with inhibitors that bound at non-canonical sites and 
bind there with different conformations. So the situation in these 
complex-structures could be a bit similar to your situation. In our case, the 
inhibitors bind on the non-canonical site with roughly Kd 5-20mM, causing their 
density to really wash out to an amount that parts of the molecule are no 
longer resolved due to the absence of deep binding pockets. I know the behavior 
you describe, namely that the molecule drifts over the epitope without creating 
difference density at the new position.
Sadly, I don't have a solution that would help you out for sure, but here are 
three tips:
- looking at the DS, I would assume that you have significant information 
beyond 1.9A (completeness is still 94% and CC1/2 way over 60%. How much more 
information can you bring into refinement? It took me a 1.1A DS to finally 
resolve the proper orientation of a weakly, non-canonically bound inhibitor, so 
it might be a good idea to extend the DS?
- try fem maps, might well be that they bring up important details to place the 
molecule (however, in refinement, the ligand will drift off again...)
- Use an alternate method to track down weak interactions. If I cannot resolve 
a complex satisfactorily, I switch to HSQC, which is much more sensible for Kds 
in the mM range. Just use it to confirm that the ligand is actually binding 
where you see the density (you can determine even Kds with that method)


Best,

Matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Katherine Lim 

Sent: Friday, December 20, 2019 5:57:02 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Potential weak binding ligand in the active site

Hi all,

I apologise in advance for the long post. I am working on solving a structure 
that looks like it could have a ligand bound in the active site. My data was 
obtained from a crystal of just the soluble domain of my protein that had been 
soaked overnight in the ligand solution. The apo crystal structure is already 
known and so I have solved my structure using phaser MR. I have attached the 
Aimless report output of my structure at the end of this email. The current R 
values I have after refinement and adding in all the waters are Rfree: 0.2413 
and Rwork: 0.1897. I can clearly see green density that is much larger (only 
disappears when I contour the Fo-Fc map to about 6 A) than in my control 
crystal that had been soaked in the same concentration of just solvent (I had 
used DMF).

I am struggling to add in my ligand as it doesn't seem like the entire ligand 
can fit in the green density. We think it may be because we have only used the 
soluble domain and so the ligand isn't held very securely since the 
transmembrane domain is missing. I have been trying to fit in smaller sections 
of it and doing an occupancy refinement. So far I have been able to get part of 
the ligand in with an occupancy of about 0.6 but after the refinement run, 
phenix.refine seems to move this part of the ligand slightly out of the area 
where I had tried to fit it into the green density. Interestingly, there isn't 
a big red density in the area that this ligand section has moved to. I would 
appreciate any advice on how I should proceed with trying to figure out if I 
have tried the correct section of the ligand and the kind of refinement 
settings to use with a weak binder.

Space Group P212121
Unit cell abc   84.76, 89.84, 91.55
unit cell alpha beta gamma  90, 90, 90

OVERALL LOW RES HIGH RES
Low res limit   45.78   45.78   1.94
High res limit  1.9 9.111.9
Rmerge  0.234   0.052   1.684
Rmeas   0.244   0.054   1.768
Rpim0.069   0.016   0.527
Total # observations663073  628236851
Total # unique  55174   579 3359
I/sigma 7.5 27.91.4
CC ½0.997   0.999   0.747
Completeness %
99  98.794.7
Multiplicity12  10.811

Katherine Lim

PhD Candidate

School of Biomedical Sciences; School of Molecular Sciences

Marshall Centre for Infectious Disease Research and Training

The University of Western Australia



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[ccp4bb] CCP4 Crystallographic School in South Africa 2020

[Carmien Tolmie]

Dear CCP4bb community,

We are pleased to announce the CCP4 Crystallographic School in South
Africa, to be held from 31 March — 08 April 2020 at the University of Cape
Town, South Africa.

The workshop will cover all aspects of protein structure solution by X-ray
crystallography, including the fundamental concepts of protein
crystallography, crystallographic data collection, processing of
diffraction data, phasing, structure refinement, validation and deposition
in the PDB, as well as an introduction to CryoEM and Electron Diffraction.

Participants will have the opportunity to collect data from their own
crystals at Diamond Light Source via remote access, in a data collection
session facilitated by Diamond beamline staff. Software covered includes
iMosflm, XDS, DIALS, BLEND, PHASER, SHELX, MrBUMP, SIMBAD, ARP/wARP, Coot,
REFMAC, Isolde, Crank2, PISA and more. This workshop is most suitable for
postgraduate students, postdoctoral researchers and early career scientists
working in structural biology.

Researchers from all countries will be considered but suitably qualified
applicants from African universities will be given preference. Online
applications are open until 25 January 2020. A total of 25 participants
will be selected. The selection results will be announced no later than 14
February, 2020. For the school program and a list of confirmed speakers,
please visit our workshop webpage at https://biophysicsworkshop.co.za/

For any more information, please contact Carmien Tolmie (
ccp4sa2...@gmail.com or carmientol...@gmail.com) or Trevor Sewell (
sewelltre...@gmail.com).

 We’re looking forward to seeing you in Cape Town next year!

Best wishes,

Carmien, Ruslan, Ronan, Gwyndaf and Trevor



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Re: [ccp4bb] Potential weak binding ligand in the active site

[00000c2488af9525-dmarc-request]

Hello, the statistics all look good apart from the R-merge and R-meas. It might be worth looking at the processing again in case it can be improved. I assume you mean rms rather than A when you say the difference density only disappears at 6 A and, if so, it must be a strong feature. Does the fragment you have refined make chemical sense, either as a possible hydrolysis product, impurity or distinct binding group? Sorry, not much helpful advice here.On 20 Dec 2019 04:57, Katherine Lim  wrote:Hi all,I apologise in advance for the long post. I am working on solving a structure that looks like it could have a ligand bound in the active site. My data was obtained from a crystal of just the soluble domain of my protein that had been soaked overnight in the ligand solution. The apo crystal structure is already known and so I have solved my structure using phaser MR. I have attached the Aimless report output of my structure at the end of this email. The current R values I have after refinement and adding in all the waters are Rfree: 0.2413 and Rwork: 0.1897.  I can clearly see green density that is much larger (only disappears when I contour the Fo-Fc map to about 6 A) than in my control crystal that had been soaked in the same concentration of just solvent (I had used DMF).I am struggling to add in my ligand as it doesn't seem like the entire ligand can fit in the green density. We think it may be because we have only used the soluble domain and so the ligand isn't held very securely since the transmembrane domain is missing. I have been trying to fit in smaller sections of it and doing an occupancy refinement. So far I have been able to get part of the ligand in with an occupancy of about 0.6 but after the refinement run, phenix.refine seems to move this part of the ligand slightly out of the area where I had tried to fit it into the green density. Interestingly, there isn't a big red density in the area that this ligand section has moved to. I would appreciate any advice on how I should proceed with trying to figure out if I have tried the correct section of the ligand and the kind of refinement settings to use with a weak binder. 



	
	
	
	
	
	



Space GroupP212121Unit cell abc84.76, 89.84, 91.55unit cell alpha beta gamma90, 90, 90OVERALLLOW RESHIGH RESLow res limit45.7845.781.94High res limit1.99.111.9Rmerge 0.2340.0521.684Rmeas0.2440.0541.768Rpim0.0690.0160.527Total # observations663073628236851Total # unique551745793359I/sigma7.527.91.4CC ½0.9970.9990.747Completeness %9998.794.7Multiplicity1210.811



Katherine Lim PhD CandidateSchool of Biomedical Sciences; School of Molecular Sciences    Marshall Centre for Infectious Disease Research and Training     The University of Western Australia    




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Re: [ccp4bb] ftp://strucbio.biologie.uni-konstanz.de/pub down?

[Kay Diederichs]

Hi Johannes,

thanks for the heads-up! We moved the FTP directory to the webserver that runs 
XDSwiki and CCP4wiki, and in the process we forgot to set the (freshly 
installed) FTP server daemon to auto-restart upon boot. This is fixed now.

thanks again,

Kay

On Fri, 20 Dec 2019 11:22:55 +0100, Johannes Cramer  
wrote:

>Dear collegues,
>
>I am trying to install xdsgui, however, I cannot access any files on the
>ftp server ftp://strucbio.biologie.uni-konstanz.de/pub.
>https://www.isitdownrightnow.com/ suggests, that it is not just me, but the
>server is really down.
>Does anyone have information about whether or when the server is back up
>and running?
>Alternatively/additionally, could anyone provide the required linux
>binaries?
>
>I wish you a nice christmas and a happy new year,
>Johannes
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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[ccp4bb] two years postdoctoral fellowship, deadline for sending the application 22/01/2020

[Benini Stefano]

Dear All,

We have a call for a two years postdoc (24k€ a year) for candidates holding a 
PhD and with experience in protein purification (experience in cloning is 
desirable but not strictly required) to carry out:

Protein purification and crystallization, structural and functional 
characterization of enzymes,.

Within the project: “SupErA - Siderophore mediated iron uptake in Erwinia 
amylovora and Aspergillus fumigatus. Towards new strategies in plant and human 
health”
you will be involved in the characterization of the biosynthetic enzymes from 
the human pathogen A. fumigatus and be part of a collaborative effort between 
the University of Bolzano, the Medical University of Innsbruck (professor 
Hubertus Haas) and the Centre for Integrated Biology, University of Trento 
(professor Sheref Mansy) to develop new molecules to be used in 
therapy/diagnostics of both the human and the plant pathogen.

interested candidates can contact me for more information on the project and 
for informal enquiries
to apply please follow the link:
https://www.unibz.it/en/home/position-calls/positions-for-academic-staff/4468-chimica-organica-dr-benini?group=18

best regards
Stefano

P.S. Bolzano is located in the Dolomites area offering many hiking, climbing 
and skiing opportunities

Stefano Benini, Ph.D. Assistant Professor
Guest editor of "Carbohydrate-Active Enzymes: Structure, Activity and Reaction 
Products 2020"
A special issue of International Journal of Molecular 
Sciences (IF 4.183) (ISSN 1422-0067). This 
special issue belongs to the section "Molecular 
Biophysics". 
https://www.mdpi.com/journal/ijms/special_issues/carbohydrate-active_enzymes_2020
 deadline for submission 30/06/2020

[https://s3.amazonaws.com/zapnito/uploads/f9805f649da7ceb38a2059ab1ce4f9bc/SciReports_EBM_Branded_Sig_v2.jpg]

https://sbenini.people.unibz.it/
“And money wasn't what I had in mind. Oh God, no, what I wanted was to do good. 
I was dying to do something good.” Saul Bellow

“I don’t like anything that’s fake and I hate pretenders!” Stefano Benini

“articolo 21 della Costituzione Italiana:  Tutti hanno diritto di manifestare 
liberamente il proprio pensiero con la parola, lo scritto e ogni altro mezzo di 
diffusione.”
*
Bioorganic chemistry and Bio-Crystallography laboratory (B2Cl)
Faculty of Science and Technology, Libera Università di Bolzano
Piazza Università, 5
39100 Bolzano, Italy
Office (room K2.14):  +39 0471 017128
Laboratory (room E.021): +39 0471 017910
Fax: +39 0471 017009
https://sbenini.people.unibz.it/
orcid.org/-0001-6299-888X

"ogni giorno in più è un giorno in meno…"

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[ccp4bb] Call open for LTP and BAG beamtime at DESY beamline P11, PETRA III, Deadline: 20.01.2020

[Anja Burkhardt]

Dear all,

Hereby I would like to invite the submission of Long-Term Projects (LTP) and 
Block Allocation Group (BAG) proposals for DESY beamline P11 at the PETRA III 
synchrotron in Hamburg.

The call is open until Monday, 20 January 2020 (until midnight local Hamburg 
time, UTC+1) and relates to beamtime to be allocated during the period 2020 
(second half) - 2022 (first half). 
Detailed information, preparation guidelines and templates for LTP and BAG 
proposals are provided here:
https://photon-science.desy.de/users_area/user_guide/select_the_proposal_type

Beamline P11 is dedicated to structural investigations of biological samples 
from atomic to micrometer length scales and currently provides two experimental 
endstations: an X-ray microscope (under construction) and a crystallography 
experiment which is in user operation since 2013.

Specific features of the P11 crystallography endstation:
• High photon flux (1.3 × 10^13 ph/s at 12 keV) at the sample position 
• Broad energy range from 5.5 - 28 keV
• Full SAD/MAD capability
• High-precision single axis goniostat
• Fast data collection, currently via Pilatus 6M detector (25 Hz frame 
rate, 154 – 2000 mm sample-to-detector distance), from March 2020 on via Eiger2 
16M detector (133 Hz frame rate)
• Fast automatic sample changer (20 s) with uni-puck compatibility and 368 
sample storage capacity
• Cryo-shutter for crystal annealing
• Beam size tunability from 4 × 9 µm² (microfocus) to 300 × 300 µm² (flat 
beam) within a minute
• Microbeam capability (4 × 9 µm² focal spot with 1.3 × 10^13 ph/s photon 
flux and 1 × 1 µm² with 2 × 10^11 ph/s)
• Serial synchrotron crystallography using liquid sample delivery like 
(tape-drive setup) and fixed targets (microporous Si-chips)
• Parallel beam option for large unit cell systems
• Data collection via Python-based GUI 
• Automated data processing with XDSAPP 
• 40 core workgroup server for fast data processing
• Wet lab for sample preparation

For detailed information about our experimental setup please visit our homepage 
http://photon-science.desy.de/facilities/petra_iii/beamlines/p11_bio_imaging_and_diffraction

On behalf of the P11 team,
Anja Burkhardt



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[ccp4bb] Open position for a Biochemist/Crystallographer at FoRx Therapeutics

[Sotirios K. Sotiriou]

Dear All,

 

FoRx Therapeutics is a recently incorporated privately-held company based in 
Basel, Switzerland. It is backed by a syndicate of investors that include the 
Novartis Venture Fund, Pfizer Ventures, M Ventures, Omega Funds and LSP Venture 
Capital. FoRx Therapeutics focuses on drugging key molecular targets involved 
in the DNA Replication Stress, as a new approach in the development of targeted 
anticancer drugs.

 

We are seeking a Biochemist/Crystallographer to crystallize protein-drug 
complexes.

 

Requirements are a PhD in Biochemistry, Structural Biology or related Field. 
Postdoc experience is optional. First author publication in a relevant journal 
is required.

 

The successful candidate for this position will be a highly motivated 
individual who can communicate effectively, contribute beyond their strict 
discipline, be flexible and responsive to the changing needs of a dynamic 
entrepreneurial organization and fit well in small agile biotech team.

 

FoRx Therapeutics encourages and supports a diverse work environment as an 
Equal Opportunity Employer, offers a stimulating work environment and a 
competitive compensation package.

 

Interested candidates should send a cover letter describing research interests 
and career goals, along with a Curriculum Vitae to:

 

h...@forxtherapeutics.com  

 

Please feel free to contact me directly.

 

Kind regards,

Sotirios

 

-- 

Sotirios K. Sotiriou, PhD

Head of Biology, FoRx Therapeutics

WSJ-350.2.03, Novartis Campus

CH-4056 Basel, Switzerland

Tel: +41 (0) 788733686

sotirios.sotir...@forxtherapeutics.com

 




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[ccp4bb] Job Advert, University of Leeds

[Goldman, Adrian]

Hi,

I have a 3-year postdoctoral position in my laboratory at Leeds for a 
structural biologist (broadly defined) to continue our work on integral 
membrane pyrophosphatases (Kellosalo et al., Science, 337 p473 (2012); Li et 
al., Nature Comm, 7, 13596 (2016); Vidilaseris et al., Sci Adv 5, eaav7574 
(2019)).

The closing date is January 18th, and further information can be found here:

To view the advert use the link below:

http://jobs.leeds.ac.uk/FBSBM1137

I have a modest sized  (about 12 people) , collaborative, enthusiastic lab 
located in the Astbury centre in Leeds.

Adrian Goldman





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[ccp4bb] PDBe workshop: Making the most of PDB data with our new graph database

[David Armstrong]

Are you looking to use PDB data more effectively to answer complex 
scientific questions? Do you have experience of accessing data 
programmatically, but want to more easily create complex data queries? 
Then you will be interested in our EBI training workshop on accessing 
PDBe and PDBe-KB data using our new graph database.



This workshop covers the use of the PDBegraph database 
to extract data for solving 
complex structural biology queries. It will introduce the PDBe graph 
database and how to write Cypher queries to retrieve data of interest. 
Workshop participants will be able to use the graph database to explore 
data relevant to their own research with support and guidance from the 
development team at PDBe.



For more information and to register, please visit 
www.ebi.ac.uk/training/events/2020/mining-pdbe-and-pdbe-kb-using-graph-database 
.



Kind Regards,

David Armstrong

--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544




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[ccp4bb] open positions at Astex

[Gabor Bunkoczi]

Dear All,

Astex has multiple positions open within the Molecular Sciences group based in 
Cambridge, UK.

Software developer/X-ray crystallography: 
http://astx.com/wp-content/uploads/2019/12/Xray-Software-Developer.pdf
Structural biologist/protein scientist: 
http://astx.com/wp-content/uploads/2019/12/Structural-Biologst-MAT-cover.pdf
Software developer/X-ray crystallography (sustaining innovation PDRA): 
http://astx.com/wp-content/uploads/2019/10/SI-Post-Doc-2019-Mol-Sci.pdf

Interested candidates should liaise with the HR department (email address can 
be found in the adverts). For informal enquiries, please feel free to contact 
me directly.

Best wishes,

Gabor Bunkoczi

Astex Pharmaceuticals
436 Cambridge Science Park
Cambridge
CB4 0QA, UK

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[ccp4bb] ftp://strucbio.biologie.uni-konstanz.de/pub down?

[Johannes Cramer]

Dear collegues,

I am trying to install xdsgui, however, I cannot access any files on the
ftp server ftp://strucbio.biologie.uni-konstanz.de/pub.
https://www.isitdownrightnow.com/ suggests, that it is not just me, but the
server is really down.
Does anyone have information about whether or when the server is back up
and running?
Alternatively/additionally, could anyone provide the required linux
binaries?

I wish you a nice christmas and a happy new year,
Johannes



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