Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb

[John Berrisford]

Dear Steve

Please can you communicate with the wwPDB curation team through the OneDep
system and we can look into specific issues with your deposition.

We report all issues back to the developers (CCP4/Refmac/Phenix/Buster and
OneDep) and they have all been very quick at fixing any problems. 

Please ensure that you are running the latest version of CCP4 as this
contains the latest updates which are required to ensure that deposition
goes smoothly. 

Hope this helps

John
PDBe

-Original Message-
From: CCP4 bulletin board  On Behalf Of
stephen.c...@rc-harwell.ac.uk
Sent: 25 September 2019 15:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Errors reading mmcif files when trying to deposit
coordinates to pdb

Dear Roberto,


I am using ccp4i at the moment, but am trying i2 to see if this corrects the
problem.  I have also tried pdb-extract as suggested by Isobel, but am still
awaiting the results.


Thanks fir the suggestions so far,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

From: Steiner, Roberto 
Sent: 25 September 2019 15:08:11
To: Carr, Stephen (MRC,RAL,RCAH)
Cc: ccp4bb
Subject: Re: [ccp4bb] Errors reading mmcif files when trying to deposit
coordinates to pdb

I assume you're using ccp4i and not i2. If you use the latter the mmcif
coords file produced should be ok.
I have had the same problem a few days ago.

Best wishes
Roberto


On 25 Sep 2019, at 15:00,
stephen.c...@rc-harwell.ac.uk
mailto:stephen.c...@rc-harwell.ac.uk>> wrote:

Dear ccp4ers,


I have refined several structures using refmac5 within ccp4i and tried to
upload the output mmcif files to the pdb in order to deposit the
coordinates/structure factors.

However, during the initial upload process when the files are scanned I get
the following errors:


ERROR - Read file 'input_file_1' failed:

syntax error at line 30421

ERROR - syntax error at line 30426

Warning - Duplicate category name chem_comp_atom at line 30428

Warning - Duplicate category name chem_comp_bond at line 30446

Warning - Duplicate category name chem_comp_angle at line 30467

ERROR - syntax error at line 30581

ERROR - syntax error at line 30585


These all lie after the coordinates in the dictionary part of the file.
When I have investigated this I cannot see any duplicated category names
that would result in the above warnings and the syntax errors are not a
result of anything obvious.  I have checked for hidden characters, found
none, and can see nothing else wrong.  Finally, line 30585 does not exist,
the file stops at 30584.


Has anyone had similar problems or any suggestions that might solve this?


Thanks,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

This email and any attachments may contain confidential, copyright and or
privileged material, and are for the use of the intended addressee only. If
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7g%3Dreserved=0

Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences
and Medicine King's College London

roberto.stei...@kcl.ac.uk
Phone 

[ccp4bb] Post-doctoral Position for X-ray crystallographer at Purdue University

[Flaherty, Daniel P]

Hello All,

I have a new position for an X-ray crystallography post-doc in my lab at Purdue 
University. This position is on a newly funded NIH grant to support 
structure-based drug discovery against a novel vancomycin-resistant 
enterococcus target that has never been characterized previously. Please see 
the ad below or visit my website to learn more and apply.

Cheers,

Dan Flaherty


Post-doctoral Position for Crystallographer to Support Drug Discovery Research


The laboratory of Dr. Daniel Flaherty in the Department of Medicinal Chemistry 
and Molecular Pharmacology at Purdue University is seeking a post-doctoral 
research associate in the field of protein X-ray crystallography to support 
drug discovery efforts against a novel antibacterial target of interest in our 
laboratory. The ideal candidate would have a PhD (or expected PhD) with 
experience in protein crystallography and a proven track record of successfully 
solving ligand-bound crystal structures. Required experience includes designing 
plasmids, cloning, mutagenesis, protein preparation, protein purification, and 
a strong background in utilizing PHENIX and COOT or other comparable software 
for structure determination. Experience designing and executing biochemical 
assays for quantifying protein interactions with small molecules, such as with 
surface plasmon resonance (SPR), is a plus. The candidate would have access to 
world-class facilities and instrumentation to support their work 
(crystallization drop-setting robots, screen optimization robots, plate imaging 
robots/hotel, walk-in plate incubator rooms, and rotating-anode home X-ray 
sources) within the Crystallography Core located in the Hockmeyer Hall of 
Structural Biology. Synchrotron data collection is also a 2-hour drive from our 
department at the Advanced Photon Source (APS) at Argonne National Laboratory. 
Other responsibilities include managing data collection time/trips, maintaining 
a laboratory notebook, assisting graduate students in crystallography, and 
manuscript preparation. This position is funded by a recently awarded grant 
from the National Institutes of Health in search of novel inhibitors for a new 
antibacterial target. The position offers a competitive salary commensurate 
upon experience plus benefits and is contingent upon meeting progress 
milestones. The successful applicant will be assessed for productivity on a 
bi-annual basis with the option of yearly renewal if agreed upon by both 
parties.

Interested candidates should submit a cover letter, CV and at least 3 
references that are familiar with the candidate’s experience and research 
potential to flahertylab.pur...@gmail.com. 
The position is open November 2019, however, start date is flexible and 
negotiable depending on the availability of the candidate. For more information 
please visit https://www.flahertylab.com/positions




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Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb

[stephen.c...@rc-harwell.ac.uk]

Dear Roberto,


I am using ccp4i at the moment, but am trying i2 to see if this corrects the 
problem.  I have also tried pdb-extract as suggested by Isobel, but am still 
awaiting the results.


Thanks fir the suggestions so far,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

From: Steiner, Roberto 
Sent: 25 September 2019 15:08:11
To: Carr, Stephen (MRC,RAL,RCAH)
Cc: ccp4bb
Subject: Re: [ccp4bb] Errors reading mmcif files when trying to deposit 
coordinates to pdb

I assume you’re using ccp4i and not i2. If you use the latter the mmcif coords 
file produced should be ok.
I have had the same problem a few days ago.

Best wishes
Roberto


On 25 Sep 2019, at 15:00, 
stephen.c...@rc-harwell.ac.uk 
mailto:stephen.c...@rc-harwell.ac.uk>> wrote:

Dear ccp4ers,


I have refined several structures using refmac5 within ccp4i and tried to 
upload the output mmcif files to the pdb in order to deposit the 
coordinates/structure factors.

However, during the initial upload process when the files are scanned I get the 
following errors:


ERROR - Read file 'input_file_1' failed:

syntax error at line 30421

ERROR - syntax error at line 30426

Warning - Duplicate category name chem_comp_atom at line 30428

Warning - Duplicate category name chem_comp_bond at line 30446

Warning - Duplicate category name chem_comp_angle at line 30467

ERROR - syntax error at line 30581

ERROR - syntax error at line 30585


These all lie after the coordinates in the dictionary part of the file.  When I 
have investigated this I cannot see any duplicated category names that would 
result in the above warnings and the syntax errors are not a result of anything 
obvious.  I have checked for hidden characters, found none, and can see nothing 
else wrong.  Finally, line 30585 does not exist, the file stops at 30584.


Has anyone had similar problems or any suggestions that might solve this?


Thanks,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorized 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 this email.

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There is no guarantee that this email 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.

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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London




This email and any attachments may contain confidential, copyright and or 
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Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb

[Peter Keller]

Without seeing the file it's hard to be definite, but the syntax error 
one line after the end of the file might suggest that some multi-line 
text earlier in the file is missing its closing '' 
terminator.


Regards,

Peter.

On 25/09/2019 15:00, stephen.c...@rc-harwell.ac.uk wrote:

Dear ccp4ers,


I have refined several structures using refmac5 within ccp4i and tried to 
upload the output mmcif files to the pdb in order to deposit the 
coordinates/structure factors.

However, during the initial upload process when the files are scanned I get the 
following errors:


ERROR - Read file 'input_file_1' failed:

syntax error at line 30421

ERROR - syntax error at line 30426

Warning - Duplicate category name chem_comp_atom at line 30428

Warning - Duplicate category name chem_comp_bond at line 30446

Warning - Duplicate category name chem_comp_angle at line 30467

ERROR - syntax error at line 30581

ERROR - syntax error at line 30585


These all lie after the coordinates in the dictionary part of the file.  When I 
have investigated this I cannot see any duplicated category names that would 
result in the above warnings and the syntax errors are not a result of anything 
obvious.  I have checked for hidden characters, found none, and can see nothing 
else wrong.  Finally, line 30585 does not exist, the file stops at 30584.


Has anyone had similar problems or any suggestions that might solve this?


Thanks,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
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--
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Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
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Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb

[Steiner, Roberto]

I assume you’re using ccp4i and not i2. If you use the latter the mmcif coords 
file produced should be ok.
I have had the same problem a few days ago.

Best wishes
Roberto


On 25 Sep 2019, at 15:00, 
stephen.c...@rc-harwell.ac.uk 
mailto:stephen.c...@rc-harwell.ac.uk>> wrote:

Dear ccp4ers,


I have refined several structures using refmac5 within ccp4i and tried to 
upload the output mmcif files to the pdb in order to deposit the 
coordinates/structure factors.

However, during the initial upload process when the files are scanned I get the 
following errors:


ERROR - Read file 'input_file_1' failed:

syntax error at line 30421

ERROR - syntax error at line 30426

Warning - Duplicate category name chem_comp_atom at line 30428

Warning - Duplicate category name chem_comp_bond at line 30446

Warning - Duplicate category name chem_comp_angle at line 30467

ERROR - syntax error at line 30581

ERROR - syntax error at line 30585


These all lie after the coordinates in the dictionary part of the file.  When I 
have investigated this I cannot see any duplicated category names that would 
result in the above warnings and the syntax errors are not a result of anything 
obvious.  I have checked for hidden characters, found none, and can see nothing 
else wrong.  Finally, line 30585 does not exist, the file stops at 30584.


Has anyone had similar problems or any suggestions that might solve this?


Thanks,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorized 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 this email.

Any views or opinions presented are solely those of the author and do not 
necessarily represent those of the Research Complex at Harwell.

There is no guarantee that this email 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.

We use an electronic filing system. Please send electronic versions of 
documents, unless paper is specifically requested.

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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London






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[ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb

[stephen.c...@rc-harwell.ac.uk]

Dear ccp4ers,


I have refined several structures using refmac5 within ccp4i and tried to 
upload the output mmcif files to the pdb in order to deposit the 
coordinates/structure factors.

However, during the initial upload process when the files are scanned I get the 
following errors:


ERROR - Read file 'input_file_1' failed:

syntax error at line 30421

ERROR - syntax error at line 30426

Warning - Duplicate category name chem_comp_atom at line 30428

Warning - Duplicate category name chem_comp_bond at line 30446

Warning - Duplicate category name chem_comp_angle at line 30467

ERROR - syntax error at line 30581

ERROR - syntax error at line 30585


These all lie after the coordinates in the dictionary part of the file.  When I 
have investigated this I cannot see any duplicated category names that would 
result in the above warnings and the syntax errors are not a result of anything 
obvious.  I have checked for hidden characters, found none, and can see nothing 
else wrong.  Finally, line 30585 does not exist, the file stops at 30584.


Has anyone had similar problems or any suggestions that might solve this?


Thanks,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorized 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 this email.

Any views or opinions presented are solely those of the author and do not 
necessarily represent those of the Research Complex at Harwell.

There is no guarantee that this email 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.

We use an electronic filing system. Please send electronic versions of 
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Re: [ccp4bb] design specs/tolerances for crystallization rooms?

[Patrick Shaw Stewart]

>  if you're in even vaguely warm or temperate regions (or seasons), cooling
> the intake air to 4C brings it to below dew point, and then condensation
> and snow are guaranteed.


I once serviced a robot in a 4C room in Singapore, which didn't seem to
have any kind of dehumidification - or maybe it had broken down.  Water was
running feely down the walls and poling on the floor, and the robot was
covered in condensation.  Every non-stainless screw on the controller,
computer, robot etc was rusty.  Interestingly, both the robot and the
computer still worked.

Patrick


On Wed, Sep 25, 2019 at 6:04 AM Frank Von Delft 
wrote:

> My colleague Opher Gileadi gave us an excellent tip when we were designing
> our 4C harvesting room, over a decade ago:  *set it to 7C*.  The crystals
> are unlikely to mind, but it's SO much more comfortable to be in for
> hours.
>
> I seem to remember he mentioned something like a comfort inflection point
> as you approach 4C.
>
> *Install low-flow fans*.  Fridge people seem to default to installing
> hurricane machines, you have to tell them that a very very small flow is
> enough.
>
> *Get strong light* - probably even those daylight things (we don't have
> them).  Being cold is miserable enough already, there's no need to compound
> it with weak light.
>
> *Vibration* - that dwindles to insignificance if the air flow goes down.
>
> *Humidity* - we installed (at considerable expense) a low humidity air
> supply - really hard to know just how much it helps, but a few years ago
> when I had it turned it off to help save energy, very quickly I heard
> complaints about snow in the liquid nitrogen becoming a major hassle.  So
> based on that set of anecdotes, I conclude it probably *is* worth having
> dry air.
>
> It's *much* cheaper though if they can design it into the building's
> infrastructure, if it's a new building;  retrofitting turned out to be
> super expensive (in our case).
>
> As dry as possible.  Look at and understand the psychrometric chart
> (google it):  if you're in even vaguely warm or temperate regions (or
> seasons), cooling the intake air to 4C brings it to below dew point, and
> then condensation and snow are guaranteed.
>
> *Size* - make it as big as you can get away with, with lots of bench and
> shelf space.  Your students will already be miserably cold, no need for
> them to be cramped too.
>
> Good luck!
> Frank
>
>
>
>
>
> On 24/09/2019 23:40, Scott, Emily wrote:
>
> Anyone out there specifically design rooms for (protein) crystallization
> at ~22 deg and 4 deg C?  If you have successes or failures and can share
> any design specs with regard to vibration, temperature, and humidity
> tolerances, it would be much appreciated to pass on to the architects for
> our new laboratory.
>
>
>
> Sincerely,
>
> Emily Scott
>
>
>
> --
>
> Emily Scott, Ph.D.
>
> Professor, Medicinal Chemistry/Pharmacology/Biophysics
>
> Faculty Director, BioNMR Core Lab
>
> University of Michigan
>
> 428 Church Street
>
> Ann Arbor, MI 48109-1065
>
> Phone:  734-764-3530
>
> https://pharmacy.umich.edu/people/scottee
>
> Lab webpage:  http://scottlab.info
>
>
>
>
>
> **
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
>
> --
>
> 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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>


-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36



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[ccp4bb] Research fellow position at Ghent Un. and the VIB (Ghent, Belgium)

[Savvas Savvides]

Dear colleagues,

please find below a published vacancy for a post-doctoral research fellow in 
structural biology in our group at Ghent University and the VIB (Ghent, 
Belgium). For a summary of our research activities please visit:
http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides-Lab.aspx 


best wishes,
Savvas
---
Savvas Savvides
VIB Center for Inflammation Research
Ghent University, Dept. Biochemistry & Microbiology
Technologiepark-Zwijnaarde 71, B-9052 Ghent (Zwijnaarde), Belgium
+32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: 
savvas.savvides_skype
http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides-Lab.aspx 





To apply please visit:
https://career012.successfactors.eu/career?company=C956575P_job_req_id=12740_ns=job_listing=JOB_SEARCH


→   Aplication deadline 05/11/2019 23:59 (Brussels time)
→   Faculty of Sciences
→   Department WE10 - Biochemistry and microbiology
→   Reference number: 201909/WE10/DA/014
 
ABOUT GHENT UNIVERSITY
 
Ghent University is a world of its own. Employing more than 8,000 people, it is 
actively involved in education and research, management and administration, and 
technical and social services on a daily basis. It is one of the largest, most 
exciting employers in the area and offers great career opportunities. With each 
of its 11 faculties and more than 100 departments offering state-of-the-art 
study programmes that are grounded in research in a wide range of academic 
fields, Ghent University is a logical choice for its employees as well as its 
students.
 
YOUR TASKS
 
At least 70% of your assignment will be spent on academic research in 
structural biology within the Unit for Structural Biology embedded in the 
Department of Biochemistry and Microbiology (WE10) and you will provide 
technical support for data acquisition and analysis in single-particle electron 
microscopy. 
You will assist in teaching activities at the Bachelor’s or Master’s level.
You will counsel Master’s students in their exercises, work placement and 
Master’s dissertation.
 
WHAT WE ARE LOOKING FOR
 
You hold a doctoral degree in Biochemistry, Biotechnology, Biophysics, 
Structural Biology or a subject considered relevant by the selection committee. 
The degree requirements need to be fulfilled at the start of your appointment.  
  For diplomas awarded outside the European Union, a certificate of 
equivalence (NARIC) must be submitted. 
You have already conducted research and acquired technical skills in electron 
microscopy (EM) and in particular cryoEM towards the determination of the 
three-dimensional structure of proteins, protein-protein, and protein-ligand 
complexes. Such research experience needs to be supported by a publication 
track record in scientific journals that subscribe to the peer-review process. 
Additional research experience in one of the following complementary methods 
within structural biology could be an advantage:
- Macromolecular X-ray Crystallography
- Small-angle X-ray Scattering
You are familiar and have practical experience with biophysical methods for the 
study of protein-protein and protein-ligand interactions (e.g. Isothermal 
Titration Calorimetry, Biolayer interferometry, Multi-angle laser light 
scattering).
You have broad practical experience in molecular biology, protein biochemistry, 
and tissue culture for the production and purification of mammalian recombinant 
proteins and complexes thereof towards structural and biophysical studies.
You have distinguished yourself as a promising researcher during your doctorate.
You are interested in coaching students in the Bachelor’s, Master’s and/or 
Advanced Master’s programmes.
 
 
WHAT WE CAN OFFER YOU
 
We offer you a three-year appointment. The appointment may be renewed once for 
three years at the most, on condition that the previous term was given a 
positive evaluation. The term of renewal begins immediately after the first 
term has expired. Attention: If you have been previously appointed as a 
postdoctoral assistant at a university within the Flemish Community, you cannot 
apply for this position.
Your appointment will start on 1 February 2020.
Your remuneration will be determined according to salary scale AAP5. More 
information about our salary scales 
.
All Ghent University staff members enjoy a number of benefits, such as a wide 
range of training and education opportunities, 38 days of paid leave, bicycle 
commuting reimbursement, ecocheques, etc. A complete overview of all our fringe 
benefits  (in Dutch).
 
INTERESTED?
 
Apply online through the e-recruitment system before the application deadline