[ccp4bb] PhD fellowship at the Faculty of Health and Medical Sciences, University of Copenhagen

[Jette Sandholm Jensen Kastrup]

PhD fellowship at the Faculty of Health and Medical Sciences, University of 
Copenhagen



We are offering a three-year PhD fellowship within a project based upon 
positive allosteric modulation of kainate receptors (KARs). The employment as 
PhD fellow is full time and for 3 years. The PhD fellowship is financed by the 
Independent Research Fund Denmark – Health Sciences and headed by Professor 
Jette Sandholm Kastrup. The fellowship is available from 1 October 2020 or as 
soon as possible thereafter. The PhD project is performed in collaboration with 
University of Liege, Belgium and University of Bordeaux, France.



The PhD fellow will manage and carry out the research project, participate in 
the education and guidance of undergraduate and graduate students, and write 
scientific publications.



Required qualifications:

•  Qualifications corresponding to a master’s degree in pharmacy, 
pharmaceutical sciences or relevant area prior to the starting date

•  A solid background in pharmacology

•  A demonstrated ability to learn new methods and research areas

•  Acceptance with harvesting brain tissue from mice

•  An ability to work both independently and in teams

•  Fluency in English and excellent communication skills



Preferred qualifications:

•  Knowledge of ionotropic glutamate receptors

•  Cell culturing

•  Two-electrode voltage clamp or patch-clamp electrophysiology

•  Radiolabel binding assays

•  Microtitre plate-based fluorescence assays

•  Expression of proteins in E. coli and purification

•  Protein crystallography

•  Analysis of molecular structures and interactions



The deadline for applications is 31 July 2020, 23.59pm CET



For a full description of the PhD fellowship and to APPLY, please visit the 
link:

https://candidate.hr-manager.net/ApplicationInit.aspx/?cid=1307=19005=152006=5=false


Professor Jette Sandholm Kastrup
Deputy Head of Department with focus on Research
Department of Drug Design and Pharmacology
Building 30, 3. floor, room 313
Faculty of Health and Medical Sciences
University of Copenhagen
Jagtvej 162
DK-2100 Copenhagen
Denmark
Phone: +45 3533 6486
Email:j...@sund.ku.dk



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[ccp4bb] B value analysis and validation tool

[Rafiga Masmaliyeva]

Dear All, 

Kindly be informed that new program for analysis and validation of 
macromolecular B values named ToBvalid is already available online.
(https://github.com/ToBvalid/tobvalid)

Please find the user guide here: 
https://github.com/ToBvalid/tobvalid/blob/master/doc/User_Guide.pdf

Here is the preprint:
https://www.biorxiv.org/content/10.1101/2020.06.17.158089v1

and previous paper of this work:
https://doi.org/10.1107/S2059798319004807

I hope you will find it useful.
Please do not hesitate to email me if you have any questions.

Best wishes, Rafiga.



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Re: [ccp4bb] AW: [ccp4bb] Cold cabinet recommendations for AKTA Pure

[Boniecki, Michal]

Hi Alan,
I think new AKTA collector can be refrigerated. If this is not an option, 
consider putting only collector in the cold cabinet and cooling down the 
buffers. Also, you can put only columns and fraction collector inside cabinet 
which has side port for such use. Although you will have to use small diameter 
out tubing to avoid sample dilution when use like this. System live will be 
shorter inside cold cabinet due to increased humidity.

Michal

On Jun 21, 2020, at 11:10, Hughes, Jonathan 
 wrote:


CAUTION: This email originated from outside of the University of Saskatchewan. 
Do not click links or open attachments unless you recognize the sender and know 
the content is safe. If in doubt, please forward suspicious emails to 
phish...@usask.ca

hi alan,
why do you want to put the thing in a cold cabinet? if you have protease 
problems, there are better ways to get rid of them than exploiting Q10. on the 
other hand, you'll increase viscosity and thus slow down the flow rates. also, 
the high humidity will reduce the lifetime of your Äkta dramatically (ours has 
been running almost continuously for 20 years at room temperature and is still 
going strong [thanks to tina!]). if you really to need to keep the sample at 4 
°C, you can put the buffer(s) on ice and cool the column with a jacket.
best
jon

Von: CCP4 bulletin board  Im Auftrag von Paula Salgado
Gesendet: Sonntag, 21. Juni 2020 18:50
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Cold cabinet recommendations for AKTA Pure

Hi Alan

We got one a few years back, from Fisher, although I think Thermo are the 
manufacturer's:

Refrigerator FRCR4504W Forma chromatography THERMO SCIENTIFIC FORMA FRCR4504W

They also arranged for a heavy metal shelf to hold the AKTA as the normal 
shelves won't hold the weight.

We only have one AKTA Pure there, with a fraction collector and the rest of the 
cabinet holds all the columns.

Hope that helps
Paula


===

Dr Paula S. Salgado
Senior Lecturer in Macromolecular Crystallography
Molecular Mechanisms of Life Lead
During the current COVID-19 crisis, my working hours tend to focus on early 
afternoons and evenings, so please bear with me if my reply is delayed and if I 
email outside your normal working hours. In any case, I do not expect a 
response outside those hours. Stay home if you're not involved in essential 
work, stay safe.


Newcastle University Biosciences Institute
Faculty of Medical Sciences
2nd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK

Tel: +44 (0)191 208 7432
Email: paula.salg...@ncl.ac.uk



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Alan Cheung mailto:alan.che...@ucl.ac.uk>>
Sent: 21 June 2020 08:12
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Cold cabinet recommendations for AKTA Pure


⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.
Dear All

Apologies for being wildly off topic, but we're trying to find a decent cold 
cabinet for 2x AKTA Pure + F9C + sample pump.  Does anyone have any 
recommendations, especially for sliding door models?

Cheers,
Alan



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Re: [ccp4bb] Ideas for improving refinement with anisotopic data.

[Gerard Bricogne]

Dear Matthew,

 You seem to have been unlucky with this data collection. STARANISO
would be prepared to see significant data extending to 2.0A along a*, 2.7A
along b*, and 1.7A along c*. The latter limit, however, involves some guess
work via the fitting by an ellipsoid of a cut-off surface that is very much
perturbed by the fact that you have a both a cusp and a truncation by the
detector edges in that direction. Without those, it looks quite probable
that you would have good solid data extending beyond 1.6A - if only you
could redo the experiment in such a way as to actually measure them ;-) .

 As Eleanor said, it is a bad idea to make decisions about data on the
basis of the "downstream" criteria you were mentioning. STARANISO is not
just a numerical program that estimates numbers and suggests some sensible
actions that it will carry out for you: it is also a 3D visualisation tool
that shows you much more about your data and its possible shortcomings than
any Table1-style numbers ever will. If there are indeed deficiencies in the
data, like here, these 3D pictures will often point out what shortcomings in
your experiment are responsible for them. In that case, a new experiment, if
feasible, is always better than any surgery on the deficient data.

 Please feel free to get in touch off-line if you would like more
details, such as patterns of outliers that we have observed.


 With best wishes,

 The STARANISO developers.

--
On Sun, Jun 21, 2020 at 05:33:53PM +0100, Eleanor Dodson wrote:
> *Please* dont throw good 1.8A data for the sake of statistics!
> You should see more detail along certain directions
> You will publish your structure providing honest details of the anisotropy
> (I hope..) but it is the map quality that matters ..
> Eleanor
> 
> On Sun, 21 Jun 2020 at 15:16, Matthew Snee <
> matthew.s...@postgrad.manchester.ac.uk> wrote:
> 
> > Hi everyone.
> >
> > I have an x ray structure that I am finishing up, and there are a few
> > ambiguous regions where the peptide is poorly resolved.
> >
> > The data is highly anisotrophic, and requires truncation to around 2.4A to
> > achieve acceptable merging stats, although there is data in the "good"
> > direction going as high as 1.8-1.9A (determined by merging stats when using
> > elliptical cutoff).
> >
> > I have tried feeding my integration outputs to STARANISO with both the
> > elliptical and spherical cutoffs, but neither produce better results than
> > Xia2 Dials, as both need to be truncated further than 2.3A before they give
> > the same refinement stats (i.e it's best to just let refmac/phenix.refine
> > deal with the anistropy).
> >
> > As I understand it, anisotrophy can lead to loss of high resolution detail
> > because weak observations from the high res shells in the bad direction are
> > down-weighted, So any tricks to improve map quality (or conversely refining
> > data with poor completeness) would be appreciated.
> >
> > I'm not holding out hope that I can deposit anything better than 2.3A, but
> > Improving the maps might really help me with some of these troublesome
> > loops :)
> >
> > Cheers
> >
> > Matthew.
> >
> > Sent from Outlook Mobile 
> >
> > --
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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[ccp4bb] AW: [ccp4bb] Cold cabinet recommendations for AKTA Pure

[Hughes, Jonathan]

hi alan,
why do you want to put the thing in a cold cabinet? if you have protease 
problems, there are better ways to get rid of them than exploiting Q10. on the 
other hand, you'll increase viscosity and thus slow down the flow rates. also, 
the high humidity will reduce the lifetime of your Äkta dramatically (ours has 
been running almost continuously for 20 years at room temperature and is still 
going strong [thanks to tina!]). if you really to need to keep the sample at 4 
°C, you can put the buffer(s) on ice and cool the column with a jacket.
best
jon

Von: CCP4 bulletin board  Im Auftrag von Paula Salgado
Gesendet: Sonntag, 21. Juni 2020 18:50
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Cold cabinet recommendations for AKTA Pure

Hi Alan

We got one a few years back, from Fisher, although I think Thermo are the 
manufacturer's:

Refrigerator FRCR4504W Forma chromatography THERMO SCIENTIFIC FORMA FRCR4504W

They also arranged for a heavy metal shelf to hold the AKTA as the normal 
shelves won't hold the weight.

We only have one AKTA Pure there, with a fraction collector and the rest of the 
cabinet holds all the columns.

Hope that helps
Paula


===

Dr Paula S. Salgado
Senior Lecturer in Macromolecular Crystallography
Molecular Mechanisms of Life Lead
During the current COVID-19 crisis, my working hours tend to focus on early 
afternoons and evenings, so please bear with me if my reply is delayed and if I 
email outside your normal working hours. In any case, I do not expect a 
response outside those hours. Stay home if you're not involved in essential 
work, stay safe.


Newcastle University Biosciences Institute
Faculty of Medical Sciences
2nd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK

Tel: +44 (0)191 208 7432
Email: paula.salg...@ncl.ac.uk



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Alan Cheung mailto:alan.che...@ucl.ac.uk>>
Sent: 21 June 2020 08:12
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Cold cabinet recommendations for AKTA Pure


⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.
Dear All

Apologies for being wildly off topic, but we're trying to find a decent cold 
cabinet for 2x AKTA Pure + F9C + sample pump.  Does anyone have any 
recommendations, especially for sliding door models?

Cheers,
Alan



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Re: [ccp4bb] Cold cabinet recommendations for AKTA Pure

[Paula Salgado]

Hi Alan

We got one a few years back, from Fisher, although I think Thermo are the 
manufacturer's:

Refrigerator FRCR4504W Forma chromatography THERMO SCIENTIFIC FORMA FRCR4504W

They also arranged for a heavy metal shelf to hold the AKTA as the normal 
shelves won't hold the weight.

We only have one AKTA Pure there, with a fraction collector and the rest of the 
cabinet holds all the columns.

Hope that helps
Paula


===

Dr Paula S. Salgado
Senior Lecturer in Macromolecular Crystallography
Molecular Mechanisms of Life Lead

During the current COVID-19 crisis, my working hours tend to focus on early 
afternoons and evenings, so please bear with me if my reply is delayed and if I 
email outside your normal working hours. In any case, I do not expect a 
response outside those hours. Stay home if you're not involved in essential 
work, stay safe.


Newcastle University Biosciences Institute
Faculty of Medical Sciences
2nd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK

Tel: +44 (0)191 208 7432
Email: paula.salg...@ncl.ac.uk



From: CCP4 bulletin board  on behalf of Alan Cheung 

Sent: 21 June 2020 08:12
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Cold cabinet recommendations for AKTA Pure


⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Dear All

Apologies for being wildly off topic, but we're trying to find a decent cold 
cabinet for 2x AKTA Pure + F9C + sample pump.  Does anyone have any 
recommendations, especially for sliding door models?

Cheers,
Alan



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Ideas for improving refinement with anisotopic data.

[Eleanor Dodson]

*Please* dont throw good 1.8A data for the sake of statistics!
You should see more detail along certain directions
You will publish your structure providing honest details of the anisotropy
(I hope..) but it is the map quality that matters ..
Eleanor

On Sun, 21 Jun 2020 at 15:16, Matthew Snee <
matthew.s...@postgrad.manchester.ac.uk> wrote:

> Hi everyone.
>
> I have an x ray structure that I am finishing up, and there are a few
> ambiguous regions where the peptide is poorly resolved.
>
> The data is highly anisotrophic, and requires truncation to around 2.4A to
> achieve acceptable merging stats, although there is data in the "good"
> direction going as high as 1.8-1.9A (determined by merging stats when using
> elliptical cutoff).
>
> I have tried feeding my integration outputs to STARANISO with both the
> elliptical and spherical cutoffs, but neither produce better results than
> Xia2 Dials, as both need to be truncated further than 2.3A before they give
> the same refinement stats (i.e it's best to just let refmac/phenix.refine
> deal with the anistropy).
>
> As I understand it, anisotrophy can lead to loss of high resolution detail
> because weak observations from the high res shells in the bad direction are
> down-weighted, So any tricks to improve map quality (or conversely refining
> data with poor completeness) would be appreciated.
>
> I'm not holding out hope that I can deposit anything better than 2.3A, but
> Improving the maps might really help me with some of these troublesome
> loops :)
>
> Cheers
>
> Matthew.
>
> Sent from Outlook Mobile 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Thanks and outcome of ([ccp4bb] Looking for method to find similar oligomeric arrangement)

[Andrew Lovering]

Dear All


Many thanks to Johann for the suggestion of Topsearch - rather pleasingly our 
tetramer is novel in the tetrameric arrangement, but each of the dimers has its 
DNA recognition helices in agreement with several hits a win all round


Bringing joy to my lockdown.


Best

Andy



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[ccp4bb] Ideas for improving refinement with anisotopic data.

[Matthew Snee]

Hi everyone.

I have an x ray structure that I am finishing up, and there are a few ambiguous 
regions where the peptide is poorly resolved.

The data is highly anisotrophic, and requires truncation to around 2.4A to 
achieve acceptable merging stats, although there is data in the "good" 
direction going as high as 1.8-1.9A (determined by merging stats when using 
elliptical cutoff).

I have tried feeding my integration outputs to STARANISO with both the 
elliptical and spherical cutoffs, but neither produce better results than Xia2 
Dials, as both need to be truncated further than 2.3A before they give the same 
refinement stats (i.e it's best to just let refmac/phenix.refine deal with the 
anistropy).

As I understand it, anisotrophy can lead to loss of high resolution detail 
because weak observations from the high res shells in the bad direction are 
down-weighted, So any tricks to improve map quality (or conversely refining 
data with poor completeness) would be appreciated.

I'm not holding out hope that I can deposit anything better than 2.3A, but 
Improving the maps might really help me with some of these troublesome loops :)

Cheers

Matthew.

Sent from Outlook Mobile



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Re: [ccp4bb] AW: [ccp4bb] Looking for method to find similar oligomeric arrangement

[Eleanor Dodson]

WEll I would use PISA first to see if the buried surface areaagrees with my
oligamer construction - that uses symmetry..
Then test SSM with the suggested oligamers..
Eleanor

On Sun, 21 Jun 2020 at 10:24, Brandstetter Johann <
johann.brandstet...@sbg.ac.at> wrote:

> Topsearch does that, https://topsearch.services.came.sbg.ac.at/
>
> Best,
>
> Hans
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Andrew
> Lovering
> *Gesendet:* Sonntag, 21. Juni 2020 10:51
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] Looking for method to find similar oligomeric
> arrangement
>
>
>
> Thanks Boaz for the SSM heads up. I was much too DALI-centric!
>
>
>
> One last point, if anyone can offer an opinion - I presume most methods
> will match but only within ASU contents.
>
>
>
> Does any approach utilize deposited "biological unit" classification or
> (better still) crystallographic symmetry operators?
>
>
>
> Best
>
> Andy
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
>
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>



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[ccp4bb] AW: [ccp4bb] Looking for method to find similar oligomeric arrangement

[Brandstetter Johann]

Topsearch does that, https://topsearch.services.came.sbg.ac.at/
Best,
Hans

Von: CCP4 bulletin board  Im Auftrag von Andrew Lovering
Gesendet: Sonntag, 21. Juni 2020 10:51
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Looking for method to find similar oligomeric arrangement


Thanks Boaz for the SSM heads up. I was much too DALI-centric!



One last point, if anyone can offer an opinion - I presume most methods will 
match but only within ASU contents.



Does any approach utilize deposited "biological unit" classification or (better 
still) crystallographic symmetry operators?



Best

Andy



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Re: [ccp4bb] Looking for method to find similar oligomeric arrangement

[Andrew Lovering]

Thanks to all of you pointing me towards ProtCID, but unless I'm mistaken this 
works only for deposited co-ordinates / PDB entries?


I was more looking for something that would take my (yet to be deposited) PDB 
file, with its inherent tetrametric hth fold, and find similar folds in similar 
arrays


Best

Andy



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Re: [ccp4bb] Looking for method to find similar oligomeric arrangement

[orly avraham]

Hi Andy,

Are you familiar with ProtCID?
http://dunbrack2.fccc.edu/ProtCiD/Default.aspx
Might be relevant.

Best,
Orly


On Sun, Jun 21, 2020 at 12:02 AM Andrew Lovering 
wrote:

> Dear colleagues,
>
>
> I have a structure of a simple, common fold (hth, dna-binding) that I
> believe has oligomerized in a different way to that observed for any
> members of the superfamily that I can reasonably analyze.
>
>
> So if I run fold comparison analysis (e.g. DALI) it will find similar
> structures on the monomeric level but what I really want is it to find hth
> structures that place each monomer in a similar position to the monomers of
> our tetramer.this seems harder to do
>
> [literature searches are slow and all yield tetramers dissimilar in nature
> to ours]
>
>
> I can of course "cheat" and turn our tetramer into a monomer (e.g. give
> the four chains the same chain ID but different residue ranges) but in
> something like DALI this would only get a hit to anything approximating the
> tetramer with a single chain protein? (I tried, this seems to be so)
>
>
> I hope its easier than I'm making out and would love to be enlightened!
>
> Best
>
> Andy
>
> --
>
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-- 

Orly Avraham, Ph.D.
Postdoctoral fellow
The lab of Prof. Oded Livnah
and the lab of Prof. Ora Schueler-Furman
The Hebrew University of Jerusalem
Israel



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Re: [ccp4bb] Looking for method to find similar oligomeric arrangement

[Andrew Lovering]

Thanks Boaz for the SSM heads up. I was much too DALI-centric!


One last point, if anyone can offer an opinion - I presume most methods will 
match but only within ASU contents.


Does any approach utilize deposited "biological unit" classification or (better 
still) crystallographic symmetry operators?


Best

Andy



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[ccp4bb] Cold cabinet recommendations for AKTA Pure

[Alan Cheung]

Dear All

Apologies for being wildly off topic, but we're trying to find a decent
cold cabinet for 2x AKTA Pure + F9C + sample pump.  Does anyone have any
recommendations, especially for sliding door models?

Cheers,
Alan



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