[ccp4bb] Postdoc positions at Princeton

[Alexei Korennykh]

Dear Students looking for postdoc opportunities:

My lab at Princeton University invites postdoc candidates to join a 
collegial research group working on


Antiviral innate immunity
Mammalian stress response
Translational regulation
Mitochondrial circadian biology
Structural biology (X-ray and high resolution cryo-EM)
RNA biology

Some reading about our lab
https://pubmed.ncbi.nlm.nih.gov/?term=korennykh=date=50
https://scholar.princeton.edu/korennykhlab/home

If interested send me an email with a brief description of yourself and 
your current research:


akore...@princeton.edu

I look forward to hearing from you.
Alexei.




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[ccp4bb] Postdoctoral position available at the Institute of Cancer Research, London UK

[Rob Van Montfort]

The Institute of Cancer Research, London, is one of the world’s most 
influential cancer research institutes, with an outstanding record of 
achievement dating back more than 100 years. Under the leadership of our Chief 
Executive, Professor Paul Workman FRS, the ICR is ranked as the UK’s leading 
academic research centre. Together with our partner The Royal Marsden, we are 
rated in the top five cancer centres globally.

The ICR is committed to attracting, developing and retaining the best minds in 
the world to join us in our mission – to make the discoveries that defeat 
cancer.

The Cancer Research UK Cancer Therapeutics Unit (CTU), within the Division of 
Cancer Therapeutics, is a multidisciplinary 'bench to bedside' centre, 
comprising around 160 staff dedicated to the discovery and development of novel 
therapeutics for the treatment of cancer. The CTU’s exciting goal is to 
discover high quality small molecule drug candidates and to progress these to 
clinical trial. All the scientific disciplines are in place to make this 
possible, including medicinal chemistry, biology, structural biology, assay 
scientists, drug metabolism and clinical specialists.
A postdoctoral position is available in Dr Rob van Montfort’s Hit Discovery and 
Structural Design Team within the CTU in Sutton. The Post-doc will be involved 
in X-ray crystallography, fragment-based screening and structure-based drug 
design and will be responsible for protein expression, purification, 
crystallisation, structure determination and structural analysis of 
protein-ligand complexes from one of the CTU’s drug discovery programmes. The 
successful candidate will also be part of the Division of Structural Biology, 
located in Chelsea, in which the structural biologists in Dr van Montfort’s 
team are embedded, and will have access to state-of-the art crystallisation 
facilities, in-house X-ray sources and excellent access to synchrotrons. The 
successful candidate will interact closely with the biology, computational 
chemistry and medicinal chemistry teams at the CTU, and will therefore be 
expected to work across the two sites in Chelsea, London and Sutton, Surrey.
Applicants must have a PhD in a biological or physical science, and experience 
in macromolecular crystallography (to include protein biochemistry, protein 
crystallisation and protein crystallography). Experience in molecular biology, 
protein expression in insect cells, structure-based drug design, and/or 
biophysics will be an advantage.
The starting salary for the position will be in the range £32,844 to £40,137 
p.a. inclusive (based on previous post-doctoral experience) and the post is 
offered on a fixed term contract of 1 year. Informal enquiries to 
rob.vanmontf...@icr.ac.uk or yann-vai.lebi...@icr.ac.uk.
Please DO NOT send your application to Dr van Montfort or Dr Le Bihan, but 
apply via the e-recruitment system on our website 
www.icr.ac.uk
For more details see: 
https://icr.tal.net/vx/lang-en-GB/mobile-0/appcentre-1/brand-4/xf-a7200b374103/candidate/so/pm/1/pl/1/opp/1110-Postdoctoral-Training-Fellow-Protein-Crystallography/en-GB


Dr. Rob van Montfort
Reader in Structural Biology and Cancer Drug Discovery
Team Leader Hit Discovery and Structural Design
Divisions of Cancer Therapeutics and Structural Biology
The Institute of Cancer Research
15 Cotswold Road
Sutton SM2 5NG
UK

Tel:
+44-(0)20-8722-4364 (Sutton)
+44-(0)20-7153-5142 (Chelsea)
Email: rob.vanmontf...@icr.ac.uk


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.




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[ccp4bb] opinions about crystal soaking service providers

[Artem Evdokimov]

Dear CCP4ers!

I would like to once again benefit from the communal wisdom and experience
of our community. Thank you in advance for your advice!

Question: we are considering engaging an external partner to perform
crystal soaking campaign(s) on our targets. In the past I've successfully
done this 'myself' (i.e. with teams of internal professionals) and had all
kinds of results ranging from awesome to bleh. Time has moved on, however,
and I know that there are several very competent teams out there (Diamond,
Crystals First, etc.) who excel at providing services of this kind (for
money).

Could you please comment, privately (since it's going to likely generate
arguments if posted in an open forum), on what external xtal-fragment
vendors have you used and what your experiences and outcomes were? In
return, I am happy to summarize the results and share them back (assuming
there are enough replies to merit a summary).

Many thanks!

Artem

- Cosmic Cats approve of this message



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Re: [ccp4bb] [ccpem] Refinements against DeepEMhancer maps

[Marin van Heel]

Dear Wout,
A suggestion from the inventor of the FRC/FSC: please read the discussions
on using non-linear refinement procedures to optimise linear metrics beyond
their defined validity range in:  "Information: to Harvest, to Have and to
Hold", by Marin van Heel & Michael Schatz.
(https://arxiv.org/abs/2009.03223)
Groet,
Marin

On Thu, Sep 10, 2020 at 4:26 PM Oosterheert, W. (Wout) 
wrote:

> Dear all,
>
>
>
> Thank you very much for the insightful comments. Intuitively I would also
> say that using a postprocessed map that is optimized to look more like a
> protein model, shouldn’t be used to real-space refine the model. Therefore,
> I’ll keep performing my real-space refinements in the experimental maps.
> That being said, I would still very much recommend DeepEMhancer for model
> building and for map visualization in ChimeraX; in my experience, the maps
> look clean and less anisotropic.
>
>
>
> Best,
>
> Wout
>
>
>
> *Wout Oosterheert; PhD Candidate; Crystal and Structural Chemistry;
> Bijvoet Center for Biomolecular Research; Utrecht University; The
> Netherlands*
>
>
>
> *From:* Collaborative Computational Project in Electron cryo-Microscopy <
> cc...@jiscmail.ac.uk> *On Behalf Of *Schmid, Michael F.
> *Sent:* Thursday, 10 September 2020 20:09
> *To:* cc...@jiscmail.ac.uk
> *Subject:* Re: [ccpem] Refinements against DeepEMhancer maps
>
>
>
> Hi-
>
> I like to remind that what we are doing in EM is not refinement, in the
> crystallographic sense, but model optimization into whatever map we are
> using.
>
> And as for the dependence on resolution, a difference of 0.2 Å (I won’t
> call it an error, since highly refined coordinates can vary this much, at a
> 2 sigma, 5%, frequency) will not be detectable in the FSC at 2.5 Å, but
> will start to give bad correlations at high resolution in a 1.2 Å map. The
> model has to be more correct at high resolution to give a good FSC than it
> has to be at low resolution, but this is obvious.
>
> Mike
>
>
>
> *From: *Collaborative Computational Project in Electron cryo-Microscopy <
> cc...@jiscmail.ac.uk> on behalf of "Pintilie, Greg" <
> 42742b50396d-dmarc-requ...@jiscmail.ac.uk>
> *Reply-To: *"Pintilie, Greg" 
> *Date: *Thursday, September 10, 2020 at 10:52 AM
> *To: *"cc...@jiscmail.ac.uk" 
> *Subject: *Re: [ccpem] Refinements against DeepEMhancer maps
>
>
>
>
>
> I fully second Marta's comment; why not use the full information to build
> a more accurate model. Just watch out for over-sharpening, it's typically
> easy to detect visually in the form of disconnected densities; unless you
> have a 1.22Å map, then disconnected densities are OK :)
>
>
>
> Whether to use in refinement is a trickier question, because you can get
> stuck in local minima easier when there is more detail. It could help to
> start refining in the less detailed map, and then move to the more detailed
> map. Use manual adjustments in Coot/ISOLDE to get out of local minima...
>
>
>
> Lastly, if we are using a real-space score, but get lower scores when
> there is more detail in real-space, then I suppose we might have some
> questions about whether that's a good score to use?
>
>
>
> Kindly,
>
>
>
> Greg
>
>
>
>
> --
>
> *From:* Collaborative Computational Project in Electron cryo-Microscopy <
> cc...@jiscmail.ac.uk> on behalf of Marta Martinez 
> *Sent:* Thursday, September 10, 2020 12:59 PM
> *To:* cc...@jiscmail.ac.uk 
> *Subject:* Re: [ccpem] Refinements against DeepEMhancer maps
>
>
>
> Hi all,
>
> I have also used DeepEMhancer, as well as other sharpening methods,
> and I usually consider sharpened maps as a good help for tracing in
> Coot. They contribute to solve quite a few ambiguities. Normally, I
> have both the experimental map (coming from Relion in your case) as
> well as the sharpened map (one or several) aligned together to
> constantly assess the reliability of the improvements of tracing that
> I can get with the sharpened maps, especially in controversial areas.
>
> Commonly, I perform the tracing in Coot based on the sharpened maps.
> Regarding refinement, in automatic refinement steps, however, I only
> consider the experimental map and all my validation scores are
> referred to that map (higher CC is normal). Nevertheless, small
> corrections of manual refinement are also performed in Coot and then
> the sharpened maps are again a good help. As you might have
> experienced, several rounds of automatic and manual refinement are
> common to constantly improve the validation scores (referred to the
> geometry of the molecule and map-model correlation). Having
> experimental and sharpened maps aligned allows you to assess the
> reliability of the improvements in tracing that you can get with the
> sharpened map.
>
> I hope this help.
>
> Best regards:
>
> MARTA
>
>
> Quoting "Oosterheert, W. (Wout)" :
>
> > Dear all,
> >
> > I’ve been playing around with map postprocessing using DeepEMhancer,
> > and I’m quite impressed by the results, 

Re: [ccp4bb] AW: Going back to Coot 0.8

[Dirk Kostrewa]

Hi Paul,

thanks - I've setup my own key bindings, already ;-)

Cheers,

Dirk.

On 11.09.20 12:34, Paul Emsley wrote:
Maybe because I've never attended a Coot course? And maybe because, 
I've even never searched for Coot tutorials because the usage of Coot 
was (almost) always very intuitive? I am open for any new developments 


OK "Pro Tip of the Day!" then...

Edit -> Settings -> Install Template Key Bindings  # you need only do 
this once.


(this is how I move around in Coot)

Fast navigation by residue: Ctrl-G {Type a number in the little box} 
Enter -> Coot jumps to that residue number


Fast navigation by blob: {Point at a blob with your mouse cursor} G -> 
Coot brings blob to screen centre




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--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
WWW:www.genzentrum.lmu.de
strubio.userweb.mwn.de
***



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Paul Emsley]

Maybe because I've never attended a Coot course? And maybe because, 
I've even never searched for Coot tutorials because the usage of Coot was (almost) always very intuitive? I 
am open for any new developments 


OK "Pro Tip of the Day!" then...

Edit -> Settings -> Install Template Key Bindings  # you need only do this once.

(this is how I move around in Coot)

Fast navigation by residue: Ctrl-G {Type a number in the little box} Enter -> 
Coot jumps to that residue number

Fast navigation by blob: {Point at a blob with your mouse cursor} G -> Coot 
brings blob to screen centre



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Frank von Delft]

I believe Paul is trying to make the caffeine materialise directly in 
your bloodstreams.


He seems to have forgotten that people actually like harvesting and 
roasing the coffee beans and folding the paper cup - so even if he 
figured out how to simulate the burning sensation in your throat as the 
hot coffee goes down, it would still frustrate a significant section of 
people.


I suspect in the long term, we'll get comfortable with just the caffeine 
hit.






On 09/09/2020 21:27, Schulz, Eike-Christian wrote:

Hi Tim,

I don't think that metaphor is quite correct. To me it seems that no matter 
what button you pushed you got coffee. In my opinion intuitive software is a 
blessing and should not easily be disregarded.

But as I said before, I am happy to read into new stuff.

Also there seem to be mixed experiences here. Might this be map-resolution 
related ?

Best,

Eike



-Original Message-
From: CCP4 bulletin board  on behalf of Georg Zocher 

Reply to: Georg Zocher 
Date: Wednesday, 9. September 2020 at 22:17
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

 Dear Herman,

 Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:
 > The old real-space refinement was intuitive and easy to use and did 
exactly what the user expected, without having to consult the manual! The result 
might not have been perfect, but was good enough for subsequent Refmac, Buster, 
Phenix refinement.

 That fits perfectly to my user experience with RSR in coot 0.8.x. and
 also explains why at least a number of people having some issues with
 the new RSR.

 All the best,

 Georg

 

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Re: [ccp4bb] AW: Going back to Coot 0.8

[Dirk Kostrewa]

Dear Paul,

I'm using Coot since its first April 2000 version and see a lot of 
improvements since then - so, really many thanks for your development!


In version 0.9, I like the much improved interface (I didn't like the 
ever growing complex Extra menu), and from a recent practical course, 
the new RSR either works marvelously or just moves residues completely 
out of density with no visual close contacts (I didn't check the probe 
clashes in the course, though ...).


The Lennard-Jones type potential might be the cause for such a 
non-obvious "mis-behaviour" of the RSR. I remember XPLOR sometimes 
blowing up the refinement because of its use of LJ potentials for VdW 
contacts and some very close contacts in the starting model. I would be 
grateful if I could switch between Lennard-Jones and harmonic potential 
in the "R/RC" settings.


I'm still convinced since the beginning of Coot, that an implementation 
of hydrogen-bond potentials in the RSR would give a huge improvement and 
probably renders the use of secondary structure restraints unnecessary.


Although I'm always interested in new method development, I must admit, 
that I've also never heard of Eigen-flip, JED-flip, backrub or CURLEW. 
Maybe because I've never attended a Coot course? And maybe because, I've 
even never searched for Coot tutorials because the usage of Coot was 
(almost) always very intuitive? I am open for any new developments - so, 
I will have a look at the pointers that you gave below. I would also be 
grateful if you could give some pointers (which I've probably 
overlooked!) where Eigen-flip, JED-flip, backrub and CURLEW are explained.


Best regards,

Dirk.

On 10.09.20 17:59, Paul Emsley wrote:

I'm not against the old style of coffee, I just don't know why anyone
would want to drink it now that the new stuff is available. I am not
against choice, it just needs to be clear to me why it is necessary.

Having thought about this a bit, I think that there are two major
differences in the real space refinement in Coot since 0.8.9.

i) The non-bonded contacts were modelled with an harmonic
   approximation and now use Lennard-Jones. The harmonic code is still
   in the source files but is not in the execution path. With a
   judicious adjustment of a few if statements, it can be
   re-established.

   For now, you can adjust the LJ weights like this:
   set_refinement_lennard_jones_epsilon(0.005)

   That will soften up the NBC and may allow some interactions that
   are repelled using the default weights.

   Also (as I said) you can use the interactive contact dots to keep
   a visual track of atom overlaps.

ii) The rigid-body "rubber-sheet" proportional neighbour drag has
    gone. Initially I thought that it was unnecessary (and normally
    that's the case), but I see that it can be useful and is now in
    0.9.1-pre.

The introductory tutorials were written a long time ago and don't
mention key-bindings ("hot keys") or interface customisation. Perhaps
they should. Here is a more modern tutorial that mentions interface
customisation:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/tutorial/Coot-Cryo-EM-basics.html 


Now that I read it, I see that it needs to be updated - Curlew is now a
full member of the Coot GUI (found under "File").

You can see me tweaking the interface in a video I did for SBGrid (it
was only meant for SBGrid attendees really):
https://www.youtube.com/watch?v=hhB8qUBBnJQ
Although note that the interface has changed (improved?) since then -
I need to redo that video.

Here is the ligand fitting/ribose rotation that I mentioned the other 
day:

https://www.youtube.com/watch?v=HTNsBBXAc78
I need to redo that video too (it was a quicky I made for Frank), but
maybe better than nothing to illustrate the utility of the new style of
atom dragging.

The multi-threaded update to the refinement was tricky to write and
now it behaves pretty stably for me but there were quite an number of
brain-twisting timing/synchronisation issues that I needed to work
out. I admit that I get "Failed: Error No Progress" more frequently
than I did when I used 0.8.x. I wonder if that's what you're seeing. I
wonder if your hardware, your map and model, your mousing skills are
tickling a race condition that I don't see (which in the coffee
analogy would be "The light is on on this new machine you've given me,
I press the button, but nothing comes out"). But then again, no one
has mentioned a bug, merely an unfamiliar behaviour. So I don't know
if the software in your hands is working as intended and we are having
a discussion about model building workflows or, rather more
prosaically, what you're seeing is just a bug.

  I had said:
  many people learnt (I discovered, rather late in the day)...

What I meant by that was two things in particular: (i) not Ctrl
dragging (as we've discussed) and (ii) (it seemed to me) that people
were asking the RSR to do too much (i.e. starting too far from where
they wanted to end up). 

Re: [ccp4bb] Relion's own implementation of motioncorr2 on gpu cluster

[mesters]

Hi,

the relion BB can be reached at cc...@jiscmail.ac.uk

To answer your question:

There are several implementations / software-packages for setting up an 
MPI on linux and if done correctly, Relion can be run on any of them 
(assuming MPI and Relion are implemented on the cluster). Login to the 
cluster and type "mpirun" in a terminal to test if the software is 
installed. Have a look at the Relion Wiki for the way to run jobs on a 
cluster:


https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Benchmarks_%26_computer_hardware#Assemble_your_own_GPU_machines

Running Relion jobs on a cluster however is not going to get the job 
done faster as the main bottlenecks are
 1) the dataset-containing HDD that will need to feed all the nodes 
with massive amounts of data (TBs rather than GBs),

 2) the speed (10G would be the minimum) & load of the network
and
 3) cluster limitations like time, nodes allocated to one job and 
overall load of the cluster

may all have a dramatic impact on the time required to get the job done.

A dedicated stand alone maschine with a modern 8-12 core processor, a 
minimum of 128MB Ram and 1 or 2 NVIDIA RTX (8GB of Ram each) will do the 
job faster. See the benchmarks on the Relion Wiki page mentioned above.


Cheers,

Jeroen




Am 11.09.20 um 01:18 schrieb Lora Sinha:
In the Relion 3.1 tutorial, the job is submitted to a local machine, 
but I wonder if I can submit the job to a GPU cluster? What MPI 
configuration should I use?





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--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/ 
Visiting 
Professorship (South Bohemian University) in Biophysics

Logo Uni Lübeck
*University of Lübeck*
Center for Structural and Cell Biology in Medicine
*Institute of Biochemistry*

Tel +49 451 3101 3105 (secretariate 3101)
Fax +49 451 3101 3104
jeroen.mest...@uni-luebeck.de 
www.biochem.uni-luebeck.de 

*Ratzeburger Allee 160
23538 Lübeck, Schleswig-Holstein
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[ccp4bb] Postdoc position in structural virology, BNITM, Hamburg, Germany

[Maria Rosenthal]

Dear CCP4 community,

I am recruiting a new postdoc to support a collaborative project between 
CSSB/HPI (Grünewald lab), EMBL Grenoble (Cusack lab) and BNITM aiming at 
solving structures of viral polymerase proteins.


Candidate profile:

 * Completed PhD in the field of biochemistry and/or structural biology
 * Strong expertise in protein expression, protein purification and
   biochemical assays
 * Fluent oral and written English
 * Excellent organizational skills and ability to plan and execute
   experiments independently and flexibly
 * Strong team spirit and excellent communication skills
 * Creative mindset and strong problem-solving capabilities
 * Experience with working in the radioactivity lab is a plus
 * Experience with common model building and structure refinement
   programs (Coot, Phenix, CCP4) is beneficial
 * Proficiency in commonly used laboratory software is expected
   (Office, PyMOL, Chimera etc.)

We offer an interesting and challenging project in a modern research 
institution and within a stimulating international collaboration, 
competitive salary included. Hamburg is a great place to live and for 
structural biology research. My team is open-minded, motivated and 
highly supportive. More about our work can be found here: 
https://www.bnitm.de/en/research/research-groups/molecular-biology-and-immunology/virology-department/biochemistry-and-structural-biology/


The position is only open for 20 months (full-time equivalent) and the 
scientist should start as soon as possible BUT the project is up and 
running.


Ready to join? -Apply! --> 
https://jobs.bnitm.de/Postdoc-mwd-full-time-or-part-time-EG-13-TV-AVH--eng-j100.html


Thank you for sharing this with potential candidates!

Kind regards,

Maria Rosenthal

--

Dr. Maria Rosenthal
- Group Leader Structural Virology -
Department of Virology

Bernhard-Nocht-Str. 74
D-20359 Hamburg
Germany
Phone:  +49 40 42818 930
Fax:+49 40 42818 931
Email:  rosent...@bnitm.de
Web:www.bnitm.de 
twitter.com/bnitm_de 
twitter.com/mariar0senthal 



Foundation under Public Law
Member of the Leibniz Association
National Reference Centre for Tropical Pathogens
Board of Directors: Prof. Dr. Egbert Tannich (Chair), Prof. Dr. Jürgen 
May, Prof. Dr. Stephan Günther, Birgit Müller (Managing Director)

Chair of the Board of Trustees: State Ministry Dr. Eva Gümbel





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