[ccp4bb] open PhD position in Bergen (Norway)

2022-05-20 Thread Petri Kursula
Hi all,
 
in a new interdisciplinary project combining machine learning, psychiatric 
disorders, drug design, protein science, and structural biology, we are looking 
for a PhD student into a fully funded 4-year position in Bergen (Norway). 
 
https://www.jobbnorge.no/en/available-jobs/job/226673/phd-position-4-years 
<https://www.jobbnorge.no/en/available-jobs/job/226673/phd-position-4-years>
 
I would be grateful if this information reaches potential candidates with a 
suitable background. I can be contacted for informal queries, but applications 
(with all required attachments) must go through the online portal.
 
Best regards,
Petri



Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
https://www.uib.no/en/persons/Petri.Kursula
petri.kurs...@uib.no
--
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
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[ccp4bb] 4-year PhD position in Bergen, Norway

2022-02-18 Thread Petri Kursula
Hi,

we have an opening for a fully funded 4-year PhD position in my group at the 
Unviersity of Bergen, Norway. The position is funded by a recent grant from the 
Norwegian Research Council, and the broad topic is the assembly and properties 
of multilayered proteolipid membranes. 

Please see the full ad below for details. Informal queries are of course 
welcome, but applications must be made through the link in the advert. Note 
that all required documents must be submitted for the application to be 
evaluated.

https://www.jobbnorge.no/en/available-jobs/job/221160/phd-position-4-years 
<https://www.jobbnorge.no/en/available-jobs/job/221160/phd-position-4-years> 

Best regards,
Petri

Petri Kursula
--
Professor 
--
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University of Bergen, Norway
https://link.uib.no/petri <https://link.uib.no/petri>
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[ccp4bb] 4-year PhD position in Bergen, Norway

2021-10-18 Thread Petri Kursula
Hi,

we have an opening for a fully funded 4-year PhD position in my group at hte 
Unviersity of Bergen, Norway. Please see the full ad below for details. 
Informal queries are welcome, but applications must be made through the link in 
the advert.

https://www.jobbnorge.no/en/available-jobs/job/213744/phd-position 

Best regards,
Petri

Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
https://link.uib.no/petri
petri.kurs...@uib.no
--
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Biocenter Oulu
University of Oulu, Finland
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[ccp4bb] Postdoc position in Bergen (Norway)

2021-09-24 Thread Petri Kursula
Hi,

we are looking for a postdoc in our project, focusing on a multidisciplinary 
approach towards formation, structure, and dynamics in proteolipid multilayer 
structures, such as seen in vertebrate myelin. As we are in the near future 
hiring several people, we are looking for an optimal combination of expertise, 
and various backgrounds related to biophysics and structural biology will be 
considered. 

The announcement, with a deadline on Oct 10th, can be found at:
https://www.jobbnorge.no/en/available-jobs/job/212348/postdoctoral-research-fellow-3-years
 
<https://www.jobbnorge.no/en/available-jobs/job/212348/postdoctoral-research-fellow-3-years>

All applications must be done through the online portal (please do attach a CV 
even though the system does not strictly require it). While applications by 
email will not be considered, informal queries are welcome.

Best regards,
Petri

Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
https://link.uib.no/petri
petri.kurs...@uib.no
--
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Biocenter Oulu
University of Oulu, Finland
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[ccp4bb] 9 PhD positions in Bergen, Norway

2021-09-10 Thread Petri Kursula
Hi all,

our faculty currently has open 9 positions for PhD students at the University 
of Bergen (Norway):

https://www.jobbnorge.no/en/available-jobs/job/211089/phd-positions-9-positions 
<https://www.jobbnorge.no/en/available-jobs/job/211089/phd-positions-9-positions>
 

Unfortunately, the application deadline is already on Sep 19th, but I wish to 
point out the Department of Biomedicine at the faculty has several groups 
working on structural biology and related topics. Any interested, qualified 
candidates should therefore contact a potential supervisor asap to prepare an 
application together. 

Best regards,
Petri


Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula
petri.kurs...@uib.no
--
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Biocenter Oulu
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Re: [ccp4bb] COOT download site

2020-06-04 Thread Petri Kursula
Could it be because that link is given at least here:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot 
<https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot>
Petri

Petri Kursula
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--
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University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula
petri.kurs...@uib.no
--
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Biocenter Oulu
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> On 4 Jun 2020, at 17:02, Jurgen Bosch  wrote:
> 
> Looks as if Clemens will be jumping straight into the future now with the new 
> link. Were you on Coot 0.069?
> 
> Jürgen 
> 
>> On Jun 4, 2020, at 10:54 AM, Paul Emsley > <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
>> 
>> On 04/06/2020 15:41, Clemens Grimm wrote:
>>> Dear All,
>>> 
>>> accessing the COOT download pages at
>>> 
>>> http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ 
>>> <http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/>
>>>  
>>> 
>>> gives me an
>>> 
>>> "The requested URL /~emsley/software/binaries/nightlies/pre-release/ was 
>>> not found on this server."
>>> 
>>> error since a few days.
>>> 
>>> Is the site down or has it moved?
>>> 
>> 
>> Good grief! I haven't thought about that web site for 10 years. I had no 
>> idea that it was alive (not that I could do anything about it if it was).
>> 
>> Google finds my Coot pages using "Emsley Coot" - well, it does for me :-)
>> 
>> 
>> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ 
>> <https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/>
>> 
>> 
>> Paul.
>> 
>> 
>> 
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Re: [ccp4bb] Covalent Cysteine Aduct

2020-03-27 Thread Petri Kursula
Looks like DTT adduct to me; but then again, if you did not have it, it 
probably is not. 
Petri

Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula
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> On 27 Mar 2020, at 22:06, Cowan, Richard H. (Dr.)  
> wrote:
> 
> Hi Robbie et al.,
> 
> I'm very sure on the crystallization conditions, but I'll check the 
> purification for BME, although it seems unlikely, since the crystallized 
> protein is a Fab.
> 
> What I would be less sure on is the age of the reagents used. Is anyone aware 
> of significant breakdown products which might be more reactive, particularly 
> the alcohols?
> 
> Thanks,
> 
> Dr Richard Cowan
> Research Associate
>  <> 
> HWLSB 1/05
> Department of Biochemistry
> University of Leicester
> Lancaster Road
> Leicester, LE1 <> 9HN <>, U.K.
>  
> Phone +44 (0) 116 229 7077
> 
> From: robbie_joos...@hotmail.com 
> Sent: 27 March 2020 20:57
> To: Cowan, Richard H. (Dr.) 
> Cc: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Covalent Cysteine Aduct
>  
> Are you absolutely sure about the conditions? The blob next to the sulfur 
> looks pretty fat so I would guess BME.
> 
> Cheers,
> Robbie
> 
> On 27 Mar 2020 21:32, "Cowan, Richard H. (Dr.)"  wrote:
> Hi All,
> 
> During the current enforced shutdown, I've been going back over some older 
> data and spotted this in one of my structures:
> 
> 
> 
> 
> It's what appears to be a covalent aduct onto a cysteine on the surface 
> (originally modeled as 2 waters!). The condition was optimized from the 
> Morpheus Screen condition D1, so MES/Imidazole pH 6.5, PEG 500MME, PEG20k and 
> a mix of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 
> 1,4-Butanediol and 1,3-Propanediol. The data has been cut at 1.7A, with good 
> stats.
> 
> Has anyone seen anything like this before? what do you think my best bet for 
> modeling this is? and aduct of 1,3-propanediol? It looks too short for 
> 1-butanol or 1,4-butandiol, and it's linear so 2-propanol and 1,2-propanediol 
> seem unlikely.
> 
> Thanks,
> 
> Dr Richard Cowan
> Research Associate
>  
> HWLSB 1/05
> Department of Biochemistry
> University of Leicester
> Lancaster Road
> Leicester, LE1 9HN, U.K.
>  
> Phone +44 (0) 116 229 7077
> 
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Re: [ccp4bb] Contradictory result between ITC and cocrystal structure

2020-02-22 Thread Petri Kursula
Hi,
a likely scenario is that your mutant crystallises in the same 
conformation/packing as the wild-type protein, and this conformation is good 
for ligand binding. In solution, your mutant protein may be more flexible/open 
than the wild-type and affinity hence lower. We see this quite often. Various 
solution structure techniques will shed light on this.

Another possibility, assuming that you did ITC only at one temperature, is that 
you are “lucky” enough to be at the temperature where enthalpy for binding is 
zero for the mutant (but not wild-type). This you can find out by carrying out 
ITC at different temperatures.
Petri
 
Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula
petri.kurs...@uib.no
--
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
--





> On 22 Feb 2020, at 07:31, monika chandravanshi 
>  wrote:
> 
> Dear All,
> 
>   I have a situation, where a mutant protein does not exhibit any 
> heat change upon titration with cognate ligand in the ITC experiment. 
> However, it co-crystallizes with the respective cognate ligand. Also, the 
> cocrystal structure reveals the conservation of the hydrogen bonding networks 
> except for the mutated residues. I would like to know the possible reason for 
> the no heat change in the ITC experiment. 
> 
> Looking forward to hearing from you.
> 
> -- 
> -
> 
> With Kind Regards
> 
> Monika Chandravanshi
> PhD Scholar, 
> Department of Biosciences and Bioengineering
> Indian Institute of Technology Guwahati, Guwahati India
> 
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Re: [ccp4bb] Cysteine sulfenic acid in coot

2019-12-10 Thread Petri Kursula
I used to always do this in a text editor - old-fashioned by fast and works :)
Petri

Petri Kursula
--
Professor 
--
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University of Bergen, Norway
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--
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University of Oulu, Finland
—



> On 10 Dec 2019, at 16:11, Sudipta Bhattacharyya 
>  wrote:
> 
> Dear community,
> 
> I would really appreciate your suggestions for linking cysteine sulfenic acid 
> (one of the active site amino acid residues in my target protein) to rest of 
> the protein chain. Let me summarize what I did so far in coot  - 
> 
> 1. I deleted the native cysteine residue at that location, then brought 
> cysteine sulfenic acid from the monomer library, then fit it in the density 
> and merged it, then ran refinement by refmac5, the entity fits really well 
> but the link is not established after the refinement . 
> 
> 2. In my version of coot (wincoot) I could not find "Extensions > Modelling > 
> Replace Residue"...option to change it.
> 
> Thanks in advance for your suggestions and happy holidays!
> 
> Best regards,
> Sudipta
> 
> 
> -- 
> Sudipta Bhattacharyya, PhD
> Assistant Professor, 
> Department of Bioscience and Bioengineering,
> Indian Institute of Technology Jodhpur,
> Rajasthan, India.
> 
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Re: [ccp4bb] SEC and MALS

2019-08-27 Thread Petri Kursula
Hi,
that's typical behaviour for an elongated/disordered molecule, given that SEC 
separates based on hydrodynamic radius, not MW.
Petri

Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
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> On 27 Aug 2019, at 07:57, Natesh Ramanathan  wrote:
> 
> Dear  Friends,
> 
> Can you share your experience with examples of MALS giving lower 
> molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg. 
> Dimer),  for the same protein sample?
> 
>   If you have/know any published paper, can you please point me to that 
> reference paper or send me the paper?
> 
> Many thanks.
> Best regards,
> Natesh  
> 
> 
> -- 
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
> 
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor, 
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram 
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
> 
> nat...@iisertvm.ac.in <mailto:nat...@iisertvm.ac.in>
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> <http://www.researcherid.com/rid/C-4488-2008>
> ORCID: http://orcid.org/-0002-1145-5962 
> <http://orcid.org/-0002-1145-5962>
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> <https://publons.com/author/1520837/ramanathan-natesh#profile>
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> 
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[ccp4bb] 4-year PhD position at Biocenter Oulu

2019-06-10 Thread Petri Kursula
Dear colleagues,

we have a 4-year PhD position available in our lab at the University of Oulu, 
Finland. The project will start in January 2020 and end in December 2023. 

The project will focus on two main topics: the structural basis of mutations 
causing human hereditary neuropathies and the molecular structure of the myelin 
membrane. Various structural biology and biophysical techniques will be 
implemented, and the project is supported by a multidisciplinary network of 
international collaborators. 

More information and a link to the online application system can be found 
through the following link:

https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=7516=en
 
<https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=7516=en>

Please feel free to contact me for informal queries; however, applications 
received by email will NOT be accepted. 

Best regards,
Petri


Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
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University of Oulu, Finland
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Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

2018-10-10 Thread Petri Kursula
Perhaps these were all mentioned already, but here are some points...looking at 
your statistics, I would definitely process it to even higher resolution, not 
lower. I understand the detector might not have been close enough for that 
(happens often nowadays). You might start seeing hydrogens, double bonds, bent 
aromatic rings, etc., which I personally think is cool :) and often also 
informative. 

Your problem might be, as mentioned, in the low-resolution data; overloads, a 
small overlapping satellite crystal, ...? Your pseudotranslation could be 
higher than the apparent one, since simultaneous twinning will partially hide 
it (and vice versa; twin tests may tell your crystal is fine, even when it is 
not). Your a and b cell edges are nearly identical. Did you try refining using 
that twin operator? What are the processing/refinement stats if you process in 
the higher symmetry?

Since you have high redundancy, did you try to process only the beginning part 
of the dataset, up to nice completeness and stats? Do you still get the high R 
factors in refinement? Are your low-resolution R factors so high already at the 
beginning of data collection? I would expect those to be around 1-2% for this 
kind of data.

Do you have a very low solvent content? This could increase your R factors.

And perhaps not the correct forum for it: did you try processing manually with 
XDS?

Having said all that, if your maps are fine, you can show what you see is 
reliable, and you can explain the high R factor, everyone should be happy :) 
even reviewer 2.

Petri


Petri Kursula
--
Professor 
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
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> On 10 Oct 2018, at 12:18, Barone, Matthias  wrote:
> 
> I agree with Pavel... if you got so many observations you dont need TLS but 
> use anisotropic adps. What I want to add is the dangerous comment to "cutting 
> back data ... to improve Rfact" Of course, if you lower the amount of 
> observations while keeping the parameters to fit constant will lower your R 
> facts. That doesnt necessarily mean you improve your model. It just means 
> that you incase the param to obs ratio - which says nothing about the 
> accuracy of your model...
> 
> 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 Pavel Afonine 
> 
> Sent: Wednesday, October 10, 2018 11:03:49 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution 
> dataset (1.05 Ang)
>  
> Hi Tony,
> 
> I always feel some people are too "greedy" with the resolution they want to 
> achieve. I mostly find that extremely high density is a pain to work with as 
> it's usually accompanied by many dual, triple conformers, a lot of noise in 
> the solvent phase that is often difficult to interpret, etc... Often you 
> spend more time on a high resolution structure that clearly shows your 
> protein, as opposed to a low resolution structure where it's difficult to 
> interpret parts of the map. Also, in most cases you REALLY don't need a 1 Ang 
> map to clearly show the overall structure of your protein, ligands, first 
> shell of solvent molecules on the surface of your protein, etc...
> 
> higher resolution typically means you have a chance to obtain a more accurate 
> atomic model of a crystal structure, which in turn may lead to a more 
> accurate interpretation of this model. I fully agree that high resolution 
> requires more modeling effort. There is still a great room for software 
> developers to provide more automation.
>  
> Your completeness is 90% in your high resolution shell, which is fine, but 
> have you checked you can clearly see most reflections for h, k and l? Maybe 
> you're missing many reflections for one of them. I would at least try cutting 
> your data back to 1.1 or 1.2 Ang, as it might dramatically improve your R 
> factors and still show everything you want to show.
> 
> Also, did you try TLS refinement?
> 
> At resolutions like 1.2A or better one normally models ADPs as anisotropic 
> for all atoms (except H), so no need to use TLS.
> 
> Pavel
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

2018-08-14 Thread Petri Kursula
Hi,
you could try picking in the cold room. Provided the temperature change does 
not kill the crystals, this sometimes worked fine for me in similar cases.
Petri


Petri Kursula
--
Professor 
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
--
Group Leader, Adjunct Professor
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--



> On 14 Aug 2018, at 20:58, Thomas Krey  wrote:
> 
> Dear crystallization experts,
>  
> We have 3D protein crystals grown from a microseed matrix screening vapor 
> diffusion experiment in either
>  
> 15% (v/v) Reagent alcohol
> HEPES Na pH 7.5
> 0.2 M MgCl2 
>  
> or in 
>  
> 27% Isopropanol
> 0.18 M MgCl2
> 90 mM HEPES Na pH 7.5
> 10% Glycerol
>  
> Upon opening the corresponding wells these crystals move quite a bit – 
> presumably due to the volatility of the alcohols. Does anyone have a good 
> suggestion to stabilize the swirling movements? Does anyone have experience, 
> whether these conditions alone can serve as cryo-protectant (i.e., do we 
> really have to fish, move into cryo solution and fish again)? 
> Any suggestion or input would be highly welcome.
>  
> Thank you very much in advance.
>  
> Thomas
>  
>  
> Prof. Dr. Thomas Krey
> Hannover Medical School  
> Institute of Virology
> Structural Virology Group
> Carl-Neuberg-Str. 1 
> D-30625 Hannover
> phone: +49 (0) 511 - 532 4308
> email: krey.tho...@mh-hannover.de <mailto:krey.tho...@mh-hannover.de>
>  
> 
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Re: [ccp4bb] 2 Open Positions (PhD Student + Post-Doc) in Oulu, Finland

2018-06-04 Thread Petri Kursula
Dear all,

I have been informed that the original links will eventually lead to the 
application system in the Finnish language, which might not be optimal for 
some. Here are links that will allow to apply in English:

post-doc
https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5769=en
 
<https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5769=en>

PhD student:
https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5770=en
 
<https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5770=en>

Sorry for the spam,
Petri




> On 31 May 2018, at 17:33, Petri Kursula  wrote:
> 
> Dear All,
> 
> my lab at the University of Oulu, Finland, has two open positions to be 
> filled in September. The positions are part of a multidisciplinary 
> collaborative project aiming at a comprehensive understanding of protein 
> structure/function and disease mechanisms in human hereditary neuropathies. 
> 
> The post-doctoral position is open for 2.5 years, and the PhD student 
> position for 4 years.
> 
> More information about the environment, project, etc., as well as links to 
> the application system can be found through the web pages below.
> 
> Post-doc:
> https://www.saimanet.com/certiahome/open_job_view.html?id=5769 
> <https://www.saimanet.com/certiahome/open_job_view.html?id=5769>
> 
> PhD student:
> https://www.saimanet.com/certiahome/open_job_view.html?id=5770 
> <https://www.saimanet.com/certiahome/open_job_view.html?id=5770>
> 
> Applications must be submitted through the electronic system, and 
> applications received by email will not be considered.
> 
> Best regards,
> Petri
> 
> 
> Petri Kursula
> --
> Professor 
> Department of Biomedicine
> University of Bergen, Norway
> http://www.uib.no/en/rg/petrikursula 
> <http://www.uib.no/en/persons/Petri.Kursula>
> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
> --
> Group Leader, Adjunct Professor
> Faculty of Biochemistry and Molecular Medicine
> University of Oulu, Finland
> --
> 
> 
> 
> 
> 




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[ccp4bb] 2 Open Positions (PhD Student + Post-Doc) in Oulu, Finland

2018-05-31 Thread Petri Kursula
Dear All,

my lab at the University of Oulu, Finland, has two open positions to be filled 
in September. The positions are part of a multidisciplinary collaborative 
project aiming at a comprehensive understanding of protein structure/function 
and disease mechanisms in human hereditary neuropathies. 

The post-doctoral position is open for 2.5 years, and the PhD student position 
for 4 years.

More information about the environment, project, etc., as well as links to the 
application system can be found through the web pages below.

Post-doc:
https://www.saimanet.com/certiahome/open_job_view.html?id=5769 
<https://www.saimanet.com/certiahome/open_job_view.html?id=5769>

PhD student:
https://www.saimanet.com/certiahome/open_job_view.html?id=5770 
<https://www.saimanet.com/certiahome/open_job_view.html?id=5770>

Applications must be submitted through the electronic system, and applications 
received by email will not be considered.

Best regards,
Petri


Petri Kursula
--
Professor 
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
--
Group Leader, Adjunct Professor
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--






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[ccp4bb] Open PhD position in Oulu (Finland)

2018-04-18 Thread Petri Kursula
Dear all,

we have an opening for a 4-year PhD student position in our  lab in Oulu 
(Finland), and we are looking for good candidates (see link below). The project 
deals with structure-function analyses of mutations in several proteins linked 
to human peripheral neuropathies (Charcot-Marie-Tooth disease). The position 
can be filled at the beginning of September 2018. 

More information can be found at:
https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5482=en
 
<https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5482=en>

Informal queries by email are welcome, but the application must be made through 
the application system described in the link above. Applications sent by email 
will not be taken into account in the evaluation.

Best regards,
Petri

Petri Kursula
--
Professor 
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
--
Group Leader, Adjunct Professor
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--

[ccp4bb] Open PhD and post-doc positions in Bergen, Norway

2017-09-09 Thread Petri Kursula
Dear all, 

our faculty in Bergen has currently open 25 PhD and 2 post-doc positions: 

https://www.jobbnorge.no/en/available-jobs/job/141891/phd-positions-25-positions
 
<https://www.jobbnorge.no/en/available-jobs/job/141891/phd-positions-25-positions>

https://www.jobbnorge.no/en/available-jobs/job/141892/postdoctoral-fellow-2-positions
 
<https://www.jobbnorge.no/en/available-jobs/job/141892/postdoctoral-fellow-2-positions>

Interested applicants should contact group leaders in the faculty (which 
includes also structural biology research groups) as soon as possible to plan 
an application, as CVs need to be pre-screened, and the application must 
include a detailed research plan, in addition to various other documents. Feel 
free to distribute the information further to those possibly interested.

Greetings from Norway,
Petri


Petri Kursula
--
Professor 
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
--
Group Leader, Adjunct Professor
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--







Re: [ccp4bb] in crystallo enzymatic activity

2017-04-14 Thread Petri Kursula
Hi,

apart from the possibilities of conformational flexibility affected by crystal 
packing, just wondering if this mutation is supposed to actually cause an 
increase or decrease in the corresponding activity (outside the context of a 
crystal)? k(cat) and K(M) measured in solution would help here. Is the pH in 
the crystal far from the optimum of the wild-type protein? Can optimal pH 
change with the mutation?

Petri

Petri Kursula
--
Professor 
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
--
Group Leader, Adjunct Professor
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--



> On 13 Apr 2017, at 17:27, Pierre Nioche <pierre.nio...@parisdescartes.fr> 
> wrote:
> 
> Dear CCP4bb,
> 
> We work on an enzyme that we crystallized with two substrates bound in the 
> active site (the reaction transform two substrates into two products). We 
> have also the structure with the two products. We are able to see densities 
> for the substrates when we collect data at different time point 
> post-crystallization (days or weeks later). There is no change over time and 
> no in crystallo enzymatic reaction despite the fact that in solution using 
> the same crystallization solution, the reaction occurs readily.
> This is not surprising and there are already many examples in the literature.
> However, when we crystallize a single amino acid variant (mutant within the 
> active site) with the same two substrates, we initially see the substrates 
> but we then observe in crystallo enzymatic activity and formation of the 
> final products over time. This structure is identical to the one determined 
> with the two products co-crystallized with the enzyme. The crystal packing 
> does not seem to be at play here.
> I understand that in crystallo activities are well documented in the 
> literature and can be induced by addition of ligands, X-rays, change in 
> oxidative environment, etc?
> Here, the substrates are present from the beginning of the crystallization 
> experiments with the same concentration. Nothing is added to the crystals 
> later on. Only the time differentiate the two type of crystals: after a 
> couple of weeks, one has the substrates in the active site (wt) while the 
> other has the products (variant).
> 
> Is anyone aware of similar examples where a variant induce in crystallo 
> enzymatic activity without perturbation of the crystal?
> 
> Thanks,
> 
> Pierre
> Dept of Pharmacology, Toxicology and cellular signaling
> Paris Descartes University



[ccp4bb] Bergen, Norway: 14 PhD and 3 post-doc positions open

2017-02-17 Thread Petri Kursula
Hi all,

The Faculty of Medicine and Dentistry in Bergen, Norway has 14 PhD student and 
3 post-doc positions available. Bergen is a beautiful, vibrant, modern 
Scandinavian city with a high standard of living, plenty of opportunities for 
outdoor activities, and good connections to the rest of Europe. 

For more details, see:

https://www.jobbnorge.no/en/available-jobs/job/134170/phd-positions-14-positions
 
<https://www.jobbnorge.no/en/available-jobs/job/134170/phd-positions-14-positions>

and

https://www.jobbnorge.no/en/available-jobs/job/134181/postdoctoral-fellow-3-positions
 
<https://www.jobbnorge.no/en/available-jobs/job/134181/postdoctoral-fellow-3-positions>

Note: the candidates for all positions must, in addition to other relevant 
documents, provide a detailed research plan linked to a research group at the 
faculty, as well as a statement from the supervisor. Hence, prior contact, well 
in time, to a research group is an absolute pre-requisite.

The newly established, ambitious structural biology groups at the Faculty 
include e.g. projects on structural neurobiology 
(http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>) and malaria parasite cytoskeleton 
and motility  (http://www.uib.no/en/rg/inari 
<http://cc.oulu.fi/~inkursul/lab>). 

Interested qualified candidates are encouraged to contact one of the the 
corresponding group leaders with their CVs as soon as possible for 
pre-screening and possible application preparation, as the application deadline 
of March 12th is approaching fast.

Contact for structural neurobiology: Petri Kursula (petri.kurs...@uib.no 
<mailto:petri.kurs...@uib.no>)
Contact for the malaria project: Inari Kursula (inari.kurs...@uib.no 
<mailto:inari.kurs...@uib.no>)

Petri Kursula
--
Professor 
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
--
Group Leader, Adjunct Professor
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--







Re: [ccp4bb] strange X-ray diffraction diagram――RNA Or Complex?

2016-10-12 Thread Petri Kursula
From your picture it looks like you have both these needle clusters and single 
needle/rod-lke crystals. The diffraction pattern you show is what you expect 
from a needle cluster (with the ring-like patterns at low resolution), a single 
needle or a larger optimized single crystal should give you no trouble. 

Petri

Petri Kursula, PhD
--
Professor of Biochemistry and Molecular Biology
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/persons/Petri.Kursula 
<http://www.uib.no/en/persons/Petri.Kursula>
petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
--
Project Leader, Docent
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
petri.kurs...@oulu.fi <mailto:petri.kurs...@oulu.fi>
--



> On 12 Oct 2016, at 08:54, Liu Rachel <liuyujie1...@hotmail.com> wrote:
> 
> 
> Dear everyone:
> 
> Recently, I suffered a problem during my research work. I purified a zinc 
> finger protein, and crystallized as a beautiful cube in a reservoir solution 
> only containing phosphate as the precipitant, no other buffer or molecules. 
> However, regardless of multiple optimization, the crystal diffracted badly 
> (7~8 Å best). I have also tried co-crystallization with dsRNA because this 
> protein can  bind to dsRNA. Then crystals grow in a new condition(2.5M 
> (NH4)2SO4,0.1M BTP,  pH7.0)and its form change to cluster of needle. But the 
> X-ray diffraction diagram is very strange(as shown in the picture). The Data 
> cannot be processed with HKL2000 either. I want to figure out, could this be 
> a RNA crystal rather than the complex?   Or is there anybody know about the 
> crystal of RNA molecular?
> 
> Thank you very much!
> 
> 
> Yujie Liu 
> Room 2071, research center in life sciences,
> China Agricultural University 
> No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  P.R. China 
> Tel: (86)-10-62734078
> 
> 



[ccp4bb] post-doc position in Oulu, Finland

2015-02-20 Thread Petri Kursula
Hi,

I’d like to bring the following position into the attention of any suitable 
candidates:

-

POSTDOCTORAL POSITION IN MOLECULAR MATERIALS RESEARCH, UNIVERSITY OF OULU, 
FINLAND

A two-year interdisciplinary postdoctoral position in molecular materials 
research is available in the Research Community of Molecular Materials 
(http://www.oulu.fi/molecularmaterials/node/25636 
http://www.oulu.fi/molecularmaterials/node/25636) at the University of Oulu 
(http://www.oulu.fi/english http://www.oulu.fi/english), Finland. The 
community consists of seven research groups in physics, biophysics, 
nanotechnology, chemistry and biochemistry, and pursues both experimental and 
theoretical/computational work. The successful applicant will conduct research 
in tight association with at least two of the participating groups. The 
specific requirements, the contact information of the groups, and the 
instructions for applying can be found in 
https://www.saimanet.com/certiahome/open_job_view.html?did=5600jc=1id=867lang=en
 
https://www.saimanet.com/certiahome/open_job_view.html?did=5600jc=1id=867lang=en
 . The deadline for applications is April 7, 2015.

-


Best regards,
Petri

Petri Kursula, PhD
--
Professor of Biochemistry and Molecular Biology
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/persons/Petri.Kursula
petri.kurs...@biomed.uib.no
--
Project Leader, Docent
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
petri.kurs...@oulu.fi
--



Re: [ccp4bb] Formulation of my own mother liquor

2014-11-24 Thread Petri Kursula
Well I think some companies make the screens from stocks, the others adjust the 
pH of the final mixture, so you might want to check the small print for the 
screen you used in the first place…

But when optimizing with your own solutions, you would in general take the easy 
way out - make good stocks and mix them as you wish. 

Petri

Petri Kursula, PhD
--
Professor of Biochemistry and Molecular Biology
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/persons/Petri.Kursula 
http://www.uib.no/en/persons/Petri.Kursula
petri.kurs...@biomed.uib.no mailto:petri.kurs...@biomed.uib.no
--
Project Leader, Docent
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
petri.kurs...@oulu.fi mailto:petri.kurs...@oulu.fi

--
 On 21 Nov 2014, at 17:48, amro selem 
 03391c09f749-dmarc-requ...@jiscmail.ac.uk wrote:
 
 Dear All,
 first i wish you nice weekend, then i wanna ask about formulation of my own 
 mother liquor, i want to optimize a condition containing
  0.2m MgCl2, 0.1m Tris , PH 8; and 20% PEG6K as pricipitant. (PACT)
 the question is , should i make a stock solution from every ingredient by 
 dissolving it in miliQ water. then mix all stuff  together  and add water 
 till final concentration with out adjusting final pH. OR dissolve the PEG in 
 pH adjusted buffer and then mix all ingredients , so the final pH will be 8.
 any suggest any idea or any one knows what the company do. 
 CHEERS
 Amr
 



Re: [ccp4bb] Removing PEG3350

2014-08-20 Thread Petri Kursula
Hi,

There is a gray area, where you would refrain from talking about low-MW 
contaminants. PEG3350 will be a highly elongated polymer, with way higher 
hydrodynamic radius than a globular molecule of the same MW. It also will bind 
a lot of H2O. Hence, it might not go through concentrators (but could actually 
get concentrated), and also could still be present in the protein fractions 
after GF. 

But I might be wrong, of course.

Petri

On 20 Aug 2014, at 20:48, Alexander Aleshin aales...@sanfordburnham.org wrote:

 Dear Remie,
 I meant application of GF as an ion exchange column. You can use special ion 
 exchange columns, but our lab often uses preparative GF columns for this 
 task.  We just load the column, keeping sample volume   the void volume. 
 Thus, we do not  concentrate a protein before an ion exchange, only after it. 
 But that is inevitable. When I am afraid to loose a protein during its 
 concentrating, I concentrate shoulders of the eluted peak first, then add a 
 central part. 
 
 My point was that it might be okay to exchange buffers by concentrating a 
 protein, but other molecules like Peg3K would not penetrate the membrane as 
 well as water or salts do, as a result their reduction in concentration will 
 be unreliable. Like, you do a 10 fold concentrating/delusion of a solution, 
 but the final concentration of PEG3K will drop only by 3 fold... 
 
 Alex
 
 On Aug 19, 2014, at 9:42 AM, Remie wrote:
 
 Hi Alex, 
 I disagree with you even though GF is always the last step in my 
 purifications. 
 Because it involves concentration before and after the GF so during the 
 concentration you can already be doing the buffer exchange.
 You use GF when you want to purify other protein impurities if they are 
 different sizes. Of course it has other uses too. But not quite practical for 
 just changing buffer also considering the amount of protein you could be 
 loosing along the process. If one is careful, centripreps are best for 
 concentrating and changing the buffer. I tell you this from experience with 
 large hard to express proteins.
 
 Best of luck,
 Remie
 
 On Aug 19, 2014, at 10:45 AM, Alexander Aleshin aales...@sanfordburnham.org 
 wrote:
 
 Remie,
 Actually, concentrating of a protein solution is not the best approach to 
 removing low MW impurities, gel filtration chromatography is  more reliable 
 and ... faster.
 
 Regards,
 Alex
 
 On Aug 19, 2014, at 7:03 AM, Remie Fawaz-Touma wrote:
 
 Hi Reza, I had to do this before. 
 
 This protocol works for any PEG and any chemical to be removed from a 
 solution: buffer exchange into the new buffer you want your protein to be in. 
 There are ways to do that by 15 mL Amicon concentrators from millipore for 
 large volumes, or if your protein is already concentrated, there are some 
 small 0.5 mL concentrators from millipore as well.
 
 The key is to keep your spinning at low speeds (concentrators manuals will 
 tell you) so you don’t precipitate or loose your protein. Check your protein 
 concentration every 2 hours just to make sure you are not loosing it on 
 concentrator surfaces and so on. 
 
 Good Luck,
 Remie
 
 On Aug 19, 2014, at 9:55 AM, Reza Khayat rkha...@ccny.cuny.edu wrote:
 
 Hi,
 
 Does anyone have a protocol for getting rid of PEG3350 from a protein sample? 
 
 Best wishes,
 Reza
 
 Reza Khayat, PhD
 Assistant Professor
 The City College of New York
 Department of Chemistry, MR-1135
 160 Convent Avenue
 New York, NY  10031
 Tel. (212) 650-6070
 www.khayatlab.org
 
 
 




[ccp4bb] post-doc/PhD student in Oulu, Finland

2013-12-19 Thread Petri Kursula
Our group at the Faculty of Biochemistry  Molecular Medicine, Biocenter Oulu 
(University of Oulu, Finland) has an opening for a post-doctoral fellow (or an 
excellent PhD student). Our project focuses on the structure and function of 
proteins involved in the formation of the vertebrate myelin sheath. Our 
research covers both high-resolution structure determination of individual 
proteins and complexes, as well as the binding of these molecules to lipid 
membranes and the analysis of multilayered membrane assembllies. A 
multidisciplinary approach is used to link the structural information from 
single molecules to the properties of the multilayered myelin membrane. As 
methods we use e.g. X-ray crystallography, X-ray and neutron 
scattering/diffraction, NMR, electron microscopy, computational methods, and 
several other biophysical techniques.

The exact research project will be planned in detail, once a suitable candidate 
has been found. Possible projects range from high-resolution structural biology 
on nervous system proteins and complexes to studies on the structure and 
dynamics of multilayered membranes. Hands-on and theoretical experience in 
protein chemistry, structural biology, biophysics, simulations of biomolecular 
systems, and/or cell biology will be highly advantageous. The ability to work 
independently and within a group, as well as the willingness to supervise 
junior colleagues, will be expected. Fluency in English (written and spoken) is 
required. Initial funding for 1 year is available; extension will be possible 
upon favourable funding decisions. 

More information from Petri Kursula (petri.kurs...@oulu.fi) and 
www.desy.de/~petri/research  www.biochem.oulu.fi/kursula. Applications, 
including CV, publication list, and contact details for 2-3 references should 
be sent by email to the above address. Screening of applications will begin 
immediately. 

---
Petri Kursula, PhD
project leader, adjunct professor
Department of Biochemistry  Biocenter Oulu, University of Oulu, Finland
Department of Chemistry, University of Hamburg/DESY, Germany
www.biochem.oulu.fi/kursula
www.desy.de/~petri/research
petri.kurs...@oulu.fi
---







[ccp4bb] PhD positions in Oulu, Finland

2013-08-12 Thread Petri Kursula
Dear all,

our university currently has an open call for 107 PhD student positions, out of 
which 15 are within the Biocenter Oulu Doctoral Programme (see below), 
including structural biology projects. I would appreciate it, if this 
information could be brought to the attention of suitable candidates.

Best regards,
Petri

---
Petri Kursula, PhD
project leader, adjunct professor
Department of Biochemistry  Biocenter Oulu, University of Oulu, Finland
Department of Chemistry, University of Hamburg/DESY, Germany
www.biochem.oulu.fi/kursula
www.desy.de/~petri/research
petri.kurs...@oulu.fi
---


--
The Biocenter Oulu Doctoral Programme (BCO-DP) is an integral part of Biocenter 
Oulu (BCO), a large multidisciplinary research institute heading the University 
of Oulu’s (UO) strategic research focus area of Biosciences and Health in Oulu, 
Finland. The scientific excellence of BCO is guaranteed by selection of the 
UO’s best bioscience and biomedical projects based on regular international 
evaluations. The research covers areas of biomedicine, molecular and cell 
biology, biochemistry, developmental biology, genetics, structural biology and 
bioinformatics in an inspiring international environment.
 
BCO-DP announces 15 University of Oulu funded doctoral student positions for 
2014-2017 in the Biosciences and Health field.
 
BCO-DP CALL A: 12 DOCTORAL STUDENTS
12 PhD positions are available in the current BCO Main Research Projects.  For 
further information, please go to the complete call announcement 
athttp://www.oulu.fi/uniogs/dppositionscall and choose Sub-call 2 
(BCO-DP/A):http://www.oulu.fi/sites/default/files/content/UniOGS_BCO-DP-A.pdf.
 
BCO-DP CALL B: 3 DOCTORAL STUDENTS
3 positions are available for a call of BRIDGE initiatives targeting 
strategically important new types of BCO or non-BCO-affiliated projects 
specifically to promote International Cooperation, Interdisciplinary projects, 
and/or National Cooperation in the Biosciences and Health focus area. For 
further information, please go to the complete call announcement at 
http://www.oulu.fi/uniogs/dppositionscall and choose Sub-call 3 (BCO-DP/B): 
http://www.oulu.fi/sites/default/files/content/UniOGS_BCO-DP-B.pdf.
 
Contact: BCO-DP Coordinator: Dr. Ritva Saastamoinen, e-mail 
ritva.saastamoinen(at)oulu.fi
 
The deadline for the applications is 16th September, 2013, 15:00 local time. 
Complete call announcement and application information are available at the 
University of Oulu Graduate School www page: 
http://www.oulu.fi/uniogs/dppositionscall and the links therein. To apply, 
please read carefully both the General Call text and the Sub-call specific text 
and follow all the instructions.
--






Re: [ccp4bb] Intra-molecular interactions

2012-11-03 Thread Petri Kursula
For some starting points, google electrostatic interactions in intrinsically 
disordered proteins. Of course they occur in IDPs; they even have 
proportionally more charged residues than folded proteins. 

Petri

On Nov 3, 2012, at 5:06 PM, Xiaodi Yu wrote:

 Dear All:
 
 I have a quick question: how common it is that electrostatic interactions are 
 involved in intra-molecular interactions, particularly in intrinsically 
 disordered proteins? Is this interaction specific and any example?
 
 Thanks,
 
 Dee
 
 Xiaodi Yu, Ph.D.
 Boston Children's Hospital 
 Dana-Farber Cancer Institute
 Harvard Medical School
 3 Blackfan
 Boston, MA 02115
 
 


---
Petri Kursula, PhD
Group Leader, Docent of Neurobiochemistry
Department of Biochemistry  Biocenter Oulu, University of Oulu, Finland
Department of Chemistry, University of Hamburg, Germany
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---



[ccp4bb] PhD positions

2011-10-16 Thread Petri Kursula
Dear all,

some current openings for PhD students, including those with interests in 
structural biology:

13 PhD student positions at Biocenter Oulu for 2012-2015
http://www.biocenter.oulu.fi/bcogs_newpositions.html

plus a kind-of re-posting of my own ad:

---

A PhD student position (3 years, starting January 2012), to use neutron 
scattering methods for studying proteins from the vertebrate myelin sheath. 
These proteins have functions e.g. in the interactions between the myelin 
sheath and the axon, and in the compaction of the multilayered myelin membrane.

The project will involve large-scale recombinant expression of myelin proteins 
and studying their structure and function using mainly neutron scattering. The 
student will focus on the structure and dynamics of myelin proteins and their 
complexes, as well as their interactions with membranes. Complementary 
experiments will be carried out using X-rays and other biochemical/biophysical 
methods.

The ideal candidate will:
- have an MSc degree in biochemistry, physics, or a related field
- have experience in recombinant protein expression and purification and/or in 
X-ray and neutron scattering methods
- be genuinely interested in using neutrons to study biological macromolecules
- be fluent in English

The selected candidate will be affiliated with the Department of Biochemistry, 
University of Oulu, Finland, but a large part of the work is expected to be 
carried out at the Centre for Structural Systems Biology (CSSB-HZI), on-site 
the DESY synchrotron campus, Hamburg, Germany. The work will also involve 
carrying out measurements at international neutron infrastructures, and will be 
carried out in close collaboration with staff at such facilities, including the 
ILL (Grenoble). 

More information about our group can be found at www.biochem.oulu.fi/kursula, 
and informal queries by email are welcome.

To apply, please send your cv, including list of publications, plus the names 
and email addresses of 2-3 referees by email to petri.kurs...@oulu.fi. The 
application deadline is October 31st, 2011, but screening of applications will 
start immediately due to the tight schedule.



---
Petri Kursula, PhD
Group Leader, Docent of Neurobiochemistry
Department of Biochemistry, University of Oulu, Finland
Department of Chemistry, University of Hamburg, Germany
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---



Re: [ccp4bb] data processing problem with ice rings

2011-10-14 Thread Petri Kursula
Your main problem is not the ice rings but a wrong lattice/indexing solution. R 
factors are very high for even low res shells and I/sigma very low. To me this 
tells you are not finding your diffraction spots at all.

First thing to try: Take more images for the indexing step and use only the 
strongest spots. And do not refine distance during indexing, as you probably 
have a pretty high mosaicity. 

Petri

On Oct 14, 2011, at 7:12 AM, ChenTiantian wrote:

 Hi there,
 I am processing a dataset which has bad ice rings (as you can see in the 
 attach png file).
 I tried both XDS and imosflm, and got similar results, it seems that adding  
 EXCLUDE_RESOLUTION_RANGE cannot get rid of the effects of the ice rings.
 the following is part of the CORRECT.LP which is the second attached file, 
 you can find more details there. 
 
   SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION
  RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR  R-FACTOR 
 COMPARED I/SIGMA   R-meas  Rmrgd-F  Anomal  SigAno   Nano
LIMIT OBSERVED  UNIQUE  POSSIBLE OF DATA   observed  expected  
 Corr
 
  4.24   371525537  5545   99.9%  46.9% 52.7%
 371502.4850.8%19.4%   -28%   0.5135136
  3.01   553449002  9840   91.5%  62.7% 65.1%
 551161.7668.3%48.1%   -28%   0.5207760
  2.46   84636   12699 12703  100.0%  67.4% 84.7%
 846341.5573.0%54.2%   -19%   0.513   12104
  2.13   97910   14743 14987   98.4% 254.5%199.3%
 979080.16   276.2%  4899.9%   -23%   0.473   14037
  1.90  110260   16846 16940   99.4% 299.2%303.3%   
 1102450.06   325.0%   -99.9%   -17%   0.422   15995
  1.74  118354   18629 18744   99.4%1062.0%   1043.6%   
 118317   -0.20  1156.4%   -99.9%   -13%   0.380   17414
  1.61  122958   20193 20331   99.3% 967.5%   1571.1%   
 1228680.10  1059.7%   987.3%-2%   0.402   18348
  1.51  125075   21554 21794   98.9% 838.9%   1355.1%   
 1249330.08   922.6%  1116.9%-1%   0.402   18977
  1.42   72057   17042 23233   73.4% 640.8%775.3%
 703910.08   732.5%   826.7%-8%   0.425   10003
 total  823746  136245144117   94.5% 166.4%166.7%   
 8215620.40   181.1%   296.7%   -15%   0.435  119774
 
 Note that I/SIGMA of each resolution shell is 2.5, so how should I do to 
 process the dataset properly? Any suggestion about this super ice rings?
 Thanks!
 
 Tiantian
 
 -- 
 Shanghai Institute of Materia Medica, Chinese Academy of Sciences
 Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park,
 Shanghai, 201203 
 csrc.pngCORRECT.LP


---
Petri Kursula, PhD
Group Leader, Docent of Neurobiochemistry
Department of Biochemistry, University of Oulu, Finland
Department of Chemistry, University of Hamburg, Germany
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---



Re: [ccp4bb] Setup pymol in Mac OS X 10.7

2011-09-21 Thread Petri Kursula
Choice #5: you can purchase a licensed version? 
Petri

On Sep 21, 2011, at 4:38 PM, Pete Meyer wrote:

 For a fourth choice, you can do a stand-alone build of PyMOL and its 
 dependencies with relatively little problem (at least on 10.6; haven't 
 upgraded yet).
 
 Pete
 
 Xiaoguang Xue wrote:
 As I know, you have 3 choices:
 1, You can apply a free educational-use-only MacPymol from the company, 
 Schrodinger, LLC. This is the easiest way, just move the MacPymol program 
 into your Program Folder.
 2,  I think you still can try to install Pymol by Fink. Just follow the wiki 
 page of Pymol.(http://www.pymolwiki.org/index.php/MAC_Install).  But there 
 is a compatible problem between Fink and Lion. There is a Lion upgrade notes 
 written by William 
 Scott(http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes). 
 Maybe it can help you.
 3, If Fink doesn't work. I think you can try to use MacPorts. It looks like 
 there is no compatible problem between MacPorts and MacOS Lion. The install 
 process is very simple (http://www.macports.org/install.php). I found 
 MacPorts still contain Pymol package, also include apbs plugin. But there is 
 no other protein xtallography software packages, like CCP4 and coot. And It 
 is impossible to install MacPorts and Fink at the same time. So If you also 
 want install CCP4 or coot from source code, it will be very inconvenient.
 Best!
 Xiaoguang Xue
 On Wed, Sep 21, 2011 at 11:04 AM, Mecy Shi 
 mecy...@gmail.commailto:mecy...@gmail.com wrote:
 Dear members,
 I want to setup pymol in Mac OS X 10.7, but I didn't do this before.
 Who can tell me how to setup and tell me the detail setup procedure.
 and if need other programs to setup this.
 Thank you very much!
 --
 Xiaoguang Xue, PhD student
 Utrecht University
 Crystal  Structural Chemistry
 Padualaan 8. Room N807
 3584 CH Utrecht
 The Netherlands
 Tel. +31-30-253-2383


---
Petri Kursula, PhD
Group Leader, Docent of Neurobiochemistry
Department of Biochemistry, University of Oulu, Finland
Department of Chemistry, University of Hamburg, Germany
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---



[ccp4bb] PhD student position

2011-06-28 Thread Petri Kursula
Dear colleagues,
I would appreciate it if you could bring this off-topic opportunity to the 
attention of any suitable candidates.
Petri

---
A PhD student position is available in the group of Dr. Petri Kursula, to use 
neutron scattering methods to study proteins specifically expressed in the 
vertebrate myelin sheath. These proteins have functions e.g. in the 
interactions between the myelin sheath and the axon, and in the compaction of 
the multilayered myelin membrane.  

The project will involve large-scale recombinant expression of myelin proteins 
and studying their structure and function using mainly neutron scattering. The 
student will focus on the structure and dynamics of myelin proteins and their 
complexes, as well as their interactions with membranes. Complementary 
experiments will be carried out using X-rays and other biochemical/biophysical 
methods.

The ideal candidate will:
- have an MSc degree in biochemistry, physics, or a related field
- have experience in recombinant protein expression and purification and/or in 
X-ray and neutron scattering methods 
- be genuinely interested in using neutrons to study biological macromolecules
- be fluent in English

The selected candidate will be affiliated with the Department of Biochemistry, 
University of Oulu, Finland, but a large part of the work is expected to be 
carried out at the Centre for Structural Systems Biology (CSSB-HZI), on-site 
the DESY synchrotron campus, Hamburg, Germany. The work will also involve 
performing measurements at international neutron infrastructures, and will be 
carried out in collaboration with staff at such facilities, including the ILL 
(Grenoble). The position will be funded by the European Spallation Source 
(ESS). 

More information about our group can be found at www.biochem.oulu.fi/kursula, 
and informal queries by email are also welcome.

To apply, please send your cv, including list of publications, plus the names 
and email addresses of 2-3 referees by email to petri.kurs...@oulu.fi. The 
application deadline is July 31st, 2011.

---
Petri Kursula, PhD
Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland)
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---



[ccp4bb] Post-doctoral position available

2011-06-27 Thread Petri Kursula
A post-doctoral position is available in the group of Dr. Petri Kursula, to 
study structure-function relationships in proteins specifically expressed in 
the myelin sheath. The targets of the project are membrane-associated myelin 
proteins, which have functions e.g. in the interactions between the myelin 
sheath and the axon, and in the compaction of the multilayered myelin membrane. 
We are specifically interested in the structures of these proteins and their 
complexes, their interactions with macromolecular and small-molecule ligands, 
as well as membranes. 

The project will involve e.g. large-scale recombinant expression of myelin 
proteins or domains thereof, their biophysical characterization, X-ray 
crystallography and other structural biology methods, as well as more specific 
methods, such as oriented CD spectroscopy and other membrane interaction 
assays. 

The ideal candidate will have:
- PhD in biochemistry/structural biology or a closely related field
- a good publication record
- significant hands-on experience in recombinant protein expression and 
large-scale purification
- a genuine interest in structural biology
- fluency in English
- experience in supervising junior colleagues

Previous work with extracellular domains or peripheral membrane proteins will 
be considered an asset, as will experience in versatile structural biology and 
biophysical methods.

The position is initially available for 1 year, with possibilities for 
extension for up to 3 years. The selected candidate will be affiliated with the 
Department of Biochemistry, University of Oulu, Finland, but a large part of 
the work is expected to be carried out at the Centre for Structural Systems 
Biology (CSSB-HZI), on-site the DESY synchrotron campus, Hamburg. 

More information about our group can be found at www.biochem.oulu.fi/kursula.

To apply, please send your cv, including list of publications, plus the names 
and email addresses of 2-3 referees by email to petri.kurs...@oulu.fi. The 
application deadline is July 31st, 2011.


---
Petri Kursula, PhD
Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland)
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---


Re: [ccp4bb] xds question

2011-02-08 Thread Petri Kursula
Hi,
oh, I'm also surprised people seem to use something else than '-3' as the 
cutoff, i.e. are throwing away data. This, obviously, brings into new light all 
the discussions (which I definitely don't wish to restart) on the 'cutoff 
values' in R(sym) and I/sI which you use to determine the 'resolution 
limit'...and gives one more thing for referees to think about/require when 
looking at Table 1. I am sure most of them, and the readers, take it for 
granted that no data were thrown out before calculating those numbers...and 
sure, the effects of actually using those data might occasionally be more 
severe than a drop of, say, 1% in the apparent overall R(sym) or an increase in 
I/sI.
Petri

On Feb 8, 2011, at 3:07 PM, Robert Immormino wrote:

 Hi,
 I've pasted below the reasons from Dan Gewirth and the HKL2000 manual
 authors for having a -3 sigma cutoff... I'll add briefly that if you
 assume the weak data has a Gaussian distribution around zero a -3
 sigma cutoff allows you to record ~99.8% of the data.
 -bob
 
 
 SIGMA CUTOFF
 
 Cutoff for rejecting measurements on input. Default = -3.0. Be very
 careful if you increase this.
 
 What is the rationale for using sigma cutoff -3.0 in SCALEPACK?
 Wouldn't you want to reject all negative intensities? Why shouldn't
 you use a sigma cutoff 1.0 or zero? The answer to these questions is
 as follows: The best estimate of I may be negative, due to background
 subtraction and background fluctuation. Negative measurements
 typically represent random fluctuations in the detector's response to
 an X-ray signal. If a measurement is highly negative (= -3[[sigma]])
 than it may be more likely the result of a mistake, rather than just
 random fluctuation.
 
 If one eliminates negative fluctuations, but not the positive ones
 before averaging, the result will be highly biased. In SCALEPACK,
 sigma cutoff is applied before averaging. If one rejects all negative
 intensities before averaging a number of things would happen:
 
   1.  The averaged intensity would always be positive;
   2.  For totally random data with redundancy 8, in a shell where
 there was no signal, , there would be on average 4 positive
 measurements, with average intensity one sigma. This is because the
 negative measurements had been thrown out. So the average of the four
 remaining measurements would be about 2 sigma! This would look like a
 resolution shell with a meaningful signal;
   3.  R-merge would be always less than the R-merge with negative
 measurements included;
   4.  A SIGMA CUTOFF of 1 would improve R-merge even more, by
 excluding even more valid measurements.
 
 Why should this worry you? Exclusion of valid measurements will
 deteriorate the final data set. One may notice an inverse relationship
 between R-merge and data quality as a function of sigma cutoff. So
 much for using R-merge as any criterion of success.
 
 Even the best (averaged) estimate of intensity may be negative. How to
 use negative I estimates in subsequent phasing and refinement steps is
 a separate story. The author of SCALEPACK suggests the following:
 
   1. You should never convert I into F.
   2. You should square Fcalc and compare it to I. Most, but not all
 of the crystallography programs do not do this. That is life. In the
 absence of the proper treatment one can do approximations. One of them
 is provided by French and also by French and Wilson. An implementation
 of their ideas is in the CCP4 program TRUNCATE. A very simplified and
 somewhat imprecise implementation of TRUNCATE is this:
 
 if I  [[sigma]](I), F=sqrt(I)
 
 if I  [[sigma]](I), F=sqrt([[sigma]](I))
 formatSIGMA CUTOFF value
 default   -3
 example   SIGMA CUTOFF -2.5
 
 referenced from:
 http://www.hkl-xray.com/hkl_web1/hkl/Scalepack_Keywords.html


---
Petri Kursula, PhD
Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland)
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---



[ccp4bb] post-doctoral position

2010-05-01 Thread Petri Kursula
A post-doctoral position is available at the Department of Biochemistry,
University of Oulu, Finland, in the group of Dr. Petri Kursula. Our work
aims at a comprehensive structure-function characterization of the various
myelin-specific proteins that play roles in the development and
functioning of the vertebrate nervous system.

The work will include recombinant expression and purification of
challenging myelin protein targets and their biochemical, biophysical, and
structural characterization. The methods used will include
crystallography, scattering methods, and protein-protein interaction
techniques.

The suitable candidate is experienced in molecular biology and protein
purification, experience with membrane proteins is a definite plus. A keen
interest in structural biology is required, as is the ability to work both
independently and as a part of a team. Fluency in English and good
communication skills are required. The candidate is not afraid to work
towards a long-term goal in a challenging project.

The University of Oulu is one of the largest universities in Finland, and
the Department of Biochemistry harbours a number of research groups and a
complete infrastructure for structural biology. Ample beamtime is
available at European infrastructures for data collection.

Applications should be sent by email to Petri Kursula
(petri.kurs...@oulu.fi) by May 12th 2010, and should include a CV,
publication list, and the contact details of 2-3 referees. More details on
the project can be obtained from www.biochem.oulu.fi/kursula, and informal
queries are welcome.


---
Petri Kursula, PhD
Academy Research Fellow (Academy of Finland)
Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland)
Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany)
www.biochem.oulu.fi/kursula
www.desy.de/~petri
petri.kurs...@oulu.fi
petri.kurs...@desy.de
---


[ccp4bb] Post-Doctoral Opportunity in Oulu, Finland

2008-05-08 Thread Petri Kursula

Post-Doctoral Opportunity in Oulu, Finland

A post-doctoral opportunity, funded by the Sigrid Juselius  
Foundation, exists in our group for an initial period of  
approximately 1 year, with possible extension. The work will involve  
structural studies on proteins important for the function of the  
human nervous system, mainly proteins from the myelin sheath.


The successful candidate will have extensive hands-on experience on  
at least some of the following: large-scale expression and  
purification of recombinant proteins, membrane protein purification  
and characterisation, protein crystallisation, X-ray crystallography,  
small-angle X-ray scattering. Any further relevant experience will  
also be considered an asset. A large number of ready-to-use  
expression clones for the target proteins exists in the lab.


The University of Oulu is the largest university in Northern Finland.  
The Department of Biochemistry is fully equipped for protein  
structural biology work, and we have frequent access to European  
synchrotrons for data collection.


To apply, please send me an email with a full CV (including list of  
publications) plus the contact details of at least two scientists for  
references.


More information can be found at www.biochem.oulu.fi/kursula.  
Informal queries by email are also welcome.


Best regards,
Petri

---
Petri Kursula, Ph.D.
Academy Research Fellow
Docent of Neurobiochemistry
Department of Biochemistry
University of Oulu
Oulu, Finland
[EMAIL PROTECTED]
cc.oulu.fi/~pkursula
www.biochem.oulu.fi/kursula
---





Re: [ccp4bb] XDS and overlaps

2008-02-21 Thread Petri Kursula

Hi,

While on the subject, a related matter that may be of relevance:  
surprisingly many people do not remove the outliers after XDS  
processing (via using the REMOVE.HKL file) and this, in certain  
cases, has its effects on the intensity distribution and 'refinability'.


Petri

On Feb 21, 2008, at 11:44 AM, Kay Diederichs wrote:


Engin Ozkan schrieb:

Hi everyone,
I have been recently relying on XDS quite a bit, but at the same  
time worrying about how XDS treats overlaps.  We had one dataset  
that both HKL2000 and Mosflm would show to have severe overlaps,  
as expected due to unit cell parameters and the unfortunate  
crystal orientation in the loop. We always ended up with  
completeness percentages in the 70's.
XDS can find the same lattice, index and scale the data, but  
yields a 100% complete mtz (and a nice structure). Without the HKL/ 
Mosflm-like GUI, it is difficult to assess the fate of the  
overlapped observations in XDS. What I could see with VIEW was  
that some observations were being divided into several ovals,  
probably different reflections, but I'm not very certain.
So, the basic question is, how does XDS treat overlaps?  I could  
not find in the documentation an answer to this question; the  
single mention of overlaps I could find tells me that XDS can  
recognize overlaps, but does not tell me if it rejects them, or  
divvies them up into separate reflections, and if that is the  
case, how does it divide them, and how reliable is that? Depending  
on how it divides the overlaps, could that affect commonly-used  
intensity stats and distributions?

Thanks,
Engin


Engin,

the basic answer is:
a) each pixel of the detector is assigned to its nearest reflection  
in reciprocal space
b) some of these pixels will mostly allow the background  
estimation, others will mostly contribute to the integration area  
(but as they are transformed into a local coordinate system there  
is not a 1:1 relationship). At this step, pixels which should be  
background but are higher than expected (due to overlap) are rejected.
c) for each reflection, the background is estimated, and the 3D  
profile is assembled from the pixels contributing to it
d) a comparison is made: for a reflection, is the percentage of its  
observed profile assembled in c) larger than some constant (called  
MINPK in XDS.INP)? If the answer is no, this reflection will be  
discarded (you could call this situation overlap).


Among other things, this means that:
a) the program does _not_ look around each reflection to detect an  
overlap situation, it just tries to gather the pixels for each  
reflection
b) as a user, when your crystal-detector distance was chosen too  
low or the reflections are very broad (resulting in generally  
strong overlap), you may reduce MINPK down to 50. This will result  
in more completeness, but you should monitor the quality of the  
resulting data. Conversely, if you raise MINPK over its default of  
75 you will discard more reflections, but the resulting dataset  
will be a bit cleaner.


The reference is
W. Kabsch (1988)  Evaluation of single-crystal X-ray diffraction  
data from a position-sensitive detector. J. Appl. Cryst. 21,  
916-924. (http://dx.doi.org/10.1107/S0021889888007903)


HTH,

Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz


---
Petri Kursula, Ph.D.
Academy Research Fellow
Docent of Neurobiochemistry
Department of Biochemistry
University of Oulu
Oulu, Finland
[EMAIL PROTECTED]
cc.oulu.fi/~pkursula
www.biochem.oulu.fi/kursula
---