[ccp4bb] Scientist job position at AbbVie

[Longenecker, Kenton L]

Hi - I'd like to draw attention of interested candidates to the following job 
opportunity with full description to apply at:
http://abbvie.referrals.selectminds.com/jobs/senior-scientist-i-ii-protein-x-ray-crystallographer-12821

Company overview:
AbbVie (NYSE:ABBV) is a global, research-driven biopharmaceutical company 
committed to developing innovative advanced therapies for some of the world's 
most complex and critical conditions. The company's mission is to use its 
expertise, dedicated people and unique approach to innovation to markedly 
improve treatments across four primary therapeutic areas: immunology, oncology, 
virology and neuroscience. In more than 75 countries, AbbVie employees are 
working every day to advance health solutions for people around the world.

Job Description:
The Structural Biology Group at AbbVie Headquarters in Lake County, Illinois, 
is seeking a highly motivated scientist to join our Structure-Based Drug 
Discovery team. The ideal candidate should have extensive hands-on experience 
in modern structural biology techniques and computational methods of molecular 
structure analysis. As part of multidisciplinary teams, the Senior Scientist 
will utilize X-ray crystallography techniques to identify ligands and provide 
insight to advance drug discovery targets through structure-based design. The 
successful candidate will contribute to drug discovery projects across the 
portfolio of AbbVie interests that also include therapeutic antibodies and 
novel biologics.



Kenton Longenecker, Ph.D.
Sr. Principal Research Scientist

AbbVie
R Discovery, DDST Structural Biology
1 N. Waukegan Road, AP10-LL
North Chicago, IL 60064
OFFICE847-938-1428
EMAIL   kenton.longenec...@abbvie.com

abbvie.com

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[ccp4bb] Post-doctoral position in chaperone structural biology in Paris

[Philippe Meyer]

Dear All,

Please find bellow the announcement for a post-doctoral positon available in 
Paris.

Best regards,

Philippe


A post-doctoral position is available to study the structural basis of 
chaperone-dependent protein translocation in the Laboratory of Molecular and 
Cellular Biology of Eukaryotes (CNRS UMR8226) at the Institut de Biologie 
Physico-Chimique in Paris, France.
Our laboratory is looking for a highly motivated post-doctoral fellow with a 
background and experience in biochemistry and structural biology. Our lab 
studies the structure and function of the molecular chaperones Hsp70 and Hsp90, 
with a particular emphasis on understanding the structural bases of chaperone 
regulation by cochaperones and small molecules. The lab projects combine 
structural techniques with functional approaches for the study of 
chaperone-dependent protein folding, assembly and translocation using 
biochemistry, biophysics and X-ray crystallography.

The project involves molecular biology, protein biochemistry and structural 
approaches by X-ray crystallography and Cryo-EM. Our lab is fully equipped for  
protein purification and is supported by the institute’s structural biology 
platform with state of the art robotics.

The Institut de Biologie Physico-Chimique (IBPC) offers a highly dynamic social 
and scientific environment in the heart of the Paris student district (Quartier 
Latin) on the Montagne Sainte Geneviève hosting the largest concentration of 
research institutions in the city.

The successful candidate must have a PhD in biochemistry or structural biology 
with a demonstrated track record of productive research, and be able to work 
independently. Previous experience in protein production and X-ray 
crystallography is highly desirable and experience in cryoEM would constitute 
an advantage.

The position opens in January 2019, Post-doc will be funded for up to two years.

Applications including a cover letter, CV, and the email addresses of two to 
three references should be made online on the CNRS employment website: 
https://emploi.cnrs.fr/Offres.aspx  . 
Please contact Philippe Meyer at me...@ibpc.fr  for 
further enquiries.


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[ccp4bb] Deadline Extended to December 9th

[Nick DeHaan]

Hi CCP4BB,

Thanks for sharing information about the AIMS Awards with your colleagues!
Many have told us they really appreciated it.

We’ve had requests for more time - so we extended the deadline to December
9th!

For anyone with a protein target of interest, the AIMS Award program can
help you discover new molecular tools, start new drug development programs,
and get published. The program is open to investigators, postdocs, and
graduate students worldwide.

*More Info*
Website: atomwise.com/aims

Flyer: 
https://www.atomwise.com/wp-content/uploads/2019/11/Atomwise-AIMS-Awards-Flyer-Fall-2019-Extended-Deadline-W1.pdf

Infographic: 
https://www.atomwise.com/wp-content/uploads/2019/10/AIMS-Infographic-Stats_Fall2019.jpg

RFP: 
http://www.atomwise.com/wp-content/uploads/2019/11/Request-for-Proposal-RFP-Fall-2019-Extended-Deadline.pdf


Please don't hesitate to reach out to me directly if you have any questions!

Best,
Nick


Nick DeHaan, MsE
*Partnering Executive*
*Atomwise*  | *Better Medicines Faster*
ᐧ

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Re: [ccp4bb] difficult molecular replacement solution

[Eleanor Dodson]

Well, trying to solve a MR structure with low homology (20%) and several
molecules is always a challenge...
Use any information you have.
How many molecules are possible/probable given the mol.wt and unit cell?
(Matthews coeff gives suggestions..) But remember solvent content can vary
from 30% to 70% and more.

 Is the structure likely to form dimers? trimers? etc. Biochemistry can
help, and the self rotation can also give clues, although it can be a pain
to interpret..

And if so is there a dimer model or trimer or whatever? May be better to
search for fewer copies of the oligmer..

But if you get some sort of reasonable solution, then start refinement and
rebuilding - if you can improve a single copy then you can use that as a
new and better search model..


I would expect bigger increases in the LLG and TGscore if the 5th and 6th
molecule were correct but maybe not..
You know you have solved it when the rebuilding bites..
\Good luck Eleanor



On Wed, 13 Nov 2019 at 17:42, Tanner, John J.  wrote:

> Dear Rob,
>
> Based on our experience with difficult MR cases, I recommend performing
> refinement on the coordinates from MR (I prefer PHENIX simulated annealing
> for this step). Then send the refined map - WITHOUT the model - to
> automated building with density modification. The auto-built model may give
> you an indication of how many chains are in the asymmetric unit. You could
> do this procedure for each of the MR solutions (N=4,5,6) and compare the
> results. Also, if you enable automatic detection of NCS during DM, you may
> find that 6 NCS operators are found even when N=4 or 5; this would give you
> confidence that N=6 is possible.
>
> Also look at the cross rotation function to see how many strong peaks are
> present. I’m sure the peaks are listed in Phaser, but it is easier for me
> to find them in the MOLREP output.  MOLREP also provides a matrix that
> tells you which cross RF peaks are related by symmetry and which are
> unique, which is helpful.
>
> And David Schuller mentioned inspecting the self-RF, which is a good idea.
>
> Finally, do you know anything about the oligomeric state of the protein?
> If it is a pentamer, N=6 seems unlikely. If it is a dimer, N=5 in P212121
> seems unlikely.
>
> Jack
>
> John J. Tanner
> Professor of Biochemistry and Chemistry
> Associate Chair of Biochemistry
> Department of Biochemistry
> University of Missouri
> 117 Schweitzer Hall
> 503 S College Avenue
> Columbia, MO 65211
> Phone: 573-884-1280
> Email: tanne...@missouri.edu
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> Office: Schlundt Annex 203A
>
> On Nov 13, 2019, at 8:33 AM, Robert S Phillips  wrote:
>
> I have been working on a protein structure which has been hard to solve by
> molecular replacement.
>
> Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
> Space group: P 21 21 21
>
> The problem is that the homologues have only ~20% identity, and there are
> multiple chains in the asymmetric unit.  The question is how many.  It
> could be 4, 5, or 6 chains.
>
> N  solvent   P
>  4  0.602   3.090.225
>  5  0.502   2.470.388
>  6  0.403   2.060.229
>
> I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all
> possible space groups, and P212121 was the best solution.  These are the
> results.
>
> N  LLG   TFZ
> 4  104.97.5
> 5  137.57.7
> 6  166.28.3
>
>  Am I correct to conclude that there are 6 chains in the asymmetric unit?
>
> Rob
>
> Robert S. Phillips
> Professor of Chemistry and of Biochemistry and Molecular Biology
> University of Georgia
> Athens, GA 30602
> Phone: (706) 542-1996
> Fax: (706) 542-9454
> E-mail: rsphill...@chem.uga.edu
> Web:  http://tryptophan.net
> 
>
> --
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>
>
>
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Re: [ccp4bb] difficult molecular replacement solution

[Jon Cooper]

I am interested to know the resolution on the basis that the better it diffracts, the lower the solvent content, generally. Have you tried Bernard Rupp's server which gives you probabilities for the No mols per AU, partly based on resolution? The LLGs look challenging - I've seen higher ones refine with only random R-free values. On 13 Nov 2019 17:42, "Tanner, John J."  wrote:
Dear Rob,


Based on our experience with difficult MR cases, I recommend performing refinement on the coordinates from MR (I prefer PHENIX simulated annealing for this step). Then send the refined map - WITHOUT the model - to automated building with density
 modification. The auto-built model may give you an indication of how many chains are in the asymmetric unit. You could do this procedure for each of the MR solutions (N=4,5,6) and compare the results. Also, if you enable automatic detection of NCS during DM,
 you may find that 6 NCS operators are found even when N=4 or 5; this would give you confidence that N=6 is possible. 


Also look at the cross rotation function to see how many strong peaks are present. I’m sure the peaks are listed in Phaser, but it is easier for me to find them in the MOLREP output.  MOLREP also provides a matrix that tells you which cross RF
 peaks are related by symmetry and which are unique, which is helpful. 


And David Schuller mentioned inspecting the self-RF, which is a good idea.


Finally, do you know anything about the oligomeric state of the protein? If it is a pentamer, N=6 seems unlikely. If it is a dimer, N=5 in P212121 seems unlikely. 


Jack 
















John J. Tanner

Professor of Biochemistry and Chemistry

Associate Chair of Biochemistry


Department of Biochemistry

University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280

Email: tannerjj@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

Lab: Schlundt Annex rooms 3,6,9, 203B, 203C

Office: Schlundt Annex 203A















On Nov 13, 2019, at 8:33 AM, Robert S Phillips  wrote:



I have been working on a protein structure which has been hard to solve by molecular replacement.  





Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
Space group: P 21 21 21





The problem is that the homologues have only ~20% identity, and there are multiple chains in the asymmetric unit.  The question is how many.  It could be 4, 5, or 6 chains.




N  solvent   P


 4      0.602           3.09            0.225             

 5      0.502           2.47            0.388        

 6      0.403           2.06            0.229              





I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all possible space groups, and P212121 was the best solution.  These are the results.




N  LLG   TFZ


4          104.9        7.5

5          137.5        7.7

6          166.2        8.3




 Am I correct to conclude that there are 6 chains in the asymmetric unit?




Rob





Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology 

University of Georgia 
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphillips@chem.uga.edu
Web:  http://tryptophan.net







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Re: [ccp4bb] difficult molecular replacement solution

[Phoebe A. Rice]

I like to try molrep with something missing from the search model so that I can 
see if the resulting map includes density for something that I know should be 
there but the computer doesn’t.  As others have pointed out, it also bolsters 
believability if the result agrees with a self-rotation function and shows nice 
packing.

~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
  Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/


From: CCP4 bulletin board  on behalf of Robert S 
Phillips 
Reply-To: Robert S Phillips 
Date: Wednesday, November 13, 2019 at 8:33 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] difficult molecular replacement solution

I have been working on a protein structure which has been hard to solve by 
molecular replacement.

Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
Space group: P 21 21 21

The problem is that the homologues have only ~20% identity, and there are 
multiple chains in the asymmetric unit.  The question is how many.  It could be 
4, 5, or 6 chains.

N  solvent   P
 4  0.602   3.090.225
 5  0.502   2.470.388
 6  0.403   2.060.229

I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all possible 
space groups, and P212121 was the best solution.  These are the results.

N  LLG   TFZ
4  104.97.5
5  137.57.7
6  166.28.3

 Am I correct to conclude that there are 6 chains in the asymmetric unit?

Rob

Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web:  
http://tryptophan.net



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Re: [ccp4bb] difficult molecular replacement solution

[Tanner, John J.]

Dear Rob,

Based on our experience with difficult MR cases, I recommend performing 
refinement on the coordinates from MR (I prefer PHENIX simulated annealing for 
this step). Then send the refined map - WITHOUT the model - to automated 
building with density modification. The auto-built model may give you an 
indication of how many chains are in the asymmetric unit. You could do this 
procedure for each of the MR solutions (N=4,5,6) and compare the results. Also, 
if you enable automatic detection of NCS during DM, you may find that 6 NCS 
operators are found even when N=4 or 5; this would give you confidence that N=6 
is possible.

Also look at the cross rotation function to see how many strong peaks are 
present. I’m sure the peaks are listed in Phaser, but it is easier for me to 
find them in the MOLREP output.  MOLREP also provides a matrix that tells you 
which cross RF peaks are related by symmetry and which are unique, which is 
helpful.

And David Schuller mentioned inspecting the self-RF, which is a good idea.

Finally, do you know anything about the oligomeric state of the protein? If it 
is a pentamer, N=6 seems unlikely. If it is a dimer, N=5 in P212121 seems 
unlikely.

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Nov 13, 2019, at 8:33 AM, Robert S Phillips 
mailto:p...@uga.edu>> wrote:

I have been working on a protein structure which has been hard to solve by 
molecular replacement.

Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
Space group: P 21 21 21

The problem is that the homologues have only ~20% identity, and there are 
multiple chains in the asymmetric unit.  The question is how many.  It could be 
4, 5, or 6 chains.

N  solvent   P
 4  0.602   3.090.225
 5  0.502   2.470.388
 6  0.403   2.060.229

I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all possible 
space groups, and P212121 was the best solution.  These are the results.

N  LLG   TFZ
4  104.97.5
5  137.57.7
6  166.28.3

 Am I correct to conclude that there are 6 chains in the asymmetric unit?

Rob

Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web:  
http://tryptophan.net


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Re: [ccp4bb] difficult molecular replacement solution

[David J. Schuller]

Have you looked at a self-rotation function? Those can sometimes be very useful 
in deciphering multiplicity.


On 2019-11-13 09:33, Robert S Phillips wrote:
I have been working on a protein structure which has been hard to solve by 
molecular replacement.

Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
Space group: P 21 21 21

The problem is that the homologues have only ~20% identity, and there are 
multiple chains in the asymmetric unit.  The question is how many.  It could be 
4, 5, or 6 chains.

N  solvent   P
 4  0.602   3.090.225
 5  0.502   2.470.388
 6  0.403   2.060.229

I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all possible 
space groups, and P212121 was the best solution.  These are the results.

N  LLG   TFZ
4  104.97.5
5  137.57.7
6  166.28.3

 Am I correct to conclude that there are 6 chains in the asymmetric unit?

Rob

Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web:  
http://tryptophan.net



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--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu



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Re: [ccp4bb] difficult molecular replacement solution

[Kay Diederichs]

Hi Rob,

the answer to the question "how many molecules are in the ASU?" is only 
available after satisfactory model building and refinement. The Phaser results 
that you show indeed suggest 6 mols/ASU, but they don't prove it. If I were 
you, I'd give the 6-molecule solution the highest priority, and start to build 
and refine. But be prepared to revise your hypothesis if you find that some of 
the molecules overlap with others.

best,
Kay

On Wed, 13 Nov 2019 14:33:04 +, Robert S Phillips  wrote:

>I have been working on a protein structure which has been hard to solve by 
>molecular replacement.
>
>Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
>Space group: P 21 21 21
>
>The problem is that the homologues have only ~20% identity, and there are 
>multiple chains in the asymmetric unit.  The question is how many.  It could 
>be 4, 5, or 6 chains.
>
>N  solvent   P
> 4  0.602   3.090.225
> 5  0.502   2.470.388
> 6  0.403   2.060.229
>
>I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all possible 
>space groups, and P212121 was the best solution.  These are the results.
>
>N  LLG   TFZ
>4  104.97.5
>5  137.57.7
>6  166.28.3
>
> Am I correct to conclude that there are 6 chains in the asymmetric unit?
>
>Rob
>
>Robert S. Phillips
>Professor of Chemistry and of Biochemistry and Molecular Biology
>University of Georgia
>Athens, GA 30602
>Phone: (706) 542-1996
>Fax: (706) 542-9454
>E-mail: rsphill...@chem.uga.edu
>Web:  
>http://tryptophan.net
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] difficult molecular replacement solution

[Roger Rowlett]

 Look at the chain packing in your solution. If the solution is grossly
correct you will notice nice solvent channels and no glaring chain-size
holes and no gross overlaps. The initial maps should look sensible, if
noisy.

If the protein is composed of likely dimers, try a search with dimer units
to simplify the search.

Good luck.

__
Roger Rowlett

On Wed, Nov 13, 2019, 10:33 AM Robert S Phillips  wrote:

> I have been working on a protein structure which has been hard to solve by
> molecular replacement.
>
> Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
> Space group: P 21 21 21
>
> The problem is that the homologues have only ~20% identity, and there are
> multiple chains in the asymmetric unit.  The question is how many.  It
> could be 4, 5, or 6 chains.
>
> N  solvent   P
>  4  0.602   3.090.225
>  5  0.502   2.470.388
>  6  0.403   2.060.229
>
> I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all
> possible space groups, and P212121 was the best solution.  These are the
> results.
>
> N  LLG   TFZ
> 4  104.97.5
> 5  137.57.7
> 6  166.28.3
>
>  Am I correct to conclude that there are 6 chains in the asymmetric unit?
>
> Rob
>
> Robert S. Phillips
> Professor of Chemistry and of Biochemistry and Molecular Biology
> University of Georgia
> Athens, GA 30602
> Phone: (706) 542-1996
> Fax: (706) 542-9454
> E-mail: rsphill...@chem.uga.edu
> Web:  http://tryptophan.net
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] difficult molecular replacement solution

[Robert S Phillips]

I have been working on a protein structure which has been hard to solve by 
molecular replacement.

Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
Space group: P 21 21 21

The problem is that the homologues have only ~20% identity, and there are 
multiple chains in the asymmetric unit.  The question is how many.  It could be 
4, 5, or 6 chains.

N  solvent   P
 4  0.602   3.090.225
 5  0.502   2.470.388
 6  0.403   2.060.229

I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all possible 
space groups, and P212121 was the best solution.  These are the results.

N  LLG   TFZ
4  104.97.5
5  137.57.7
6  166.28.3

 Am I correct to conclude that there are 6 chains in the asymmetric unit?

Rob

Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web:  
http://tryptophan.net



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Re: [ccp4bb] CCP4MG cannot save images in Mac OS

[Stuart McNicholas]

Dear Jerome,
   Jon Agirre has pointed to me out you wrote "render" not "screenshot",
which will be independent of graphics chip. Thank you, Jon!

However, I just tried render and that seems to work as well.

Did you install CCP4MG before or after upgrading to Catalina? Or was this a
new computer onto which you've installed CCP4MG? I guess write permissions
may vary in the various cases.

Best wishes,
Stuart


On Wed, 13 Nov 2019 at 12:06, Jon Agirre  wrote:

> He mentions 'render' - perhaps he means he's used the Render menu option?
>
> On Wed, 13 Nov 2019 at 11:58, Stuart McNicholas <
> 19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Dear Jerome,
>>On my 13in Mid 2014 MacBook Pro with Intel Iris Graphics now running
>> Catalina (10.15.1), CCP4MG screenshots seem to work fine. What
>> Computer/Graphics chip are you using? I'll have to try upgrading a
>> different computer to see if I can reproduce the problem.
>>
>> Best wishes,
>> Stuart
>>
>>
>> On Wed, 13 Nov 2019 at 08:56, Stuart McNicholas <
>> stuart.mcnicho...@york.ac.uk> wrote:
>>
>>> Dear Jerome,
>>>It is entirely possible that this is a Catalina problem. I do not
>>> have a Catalina machine and hence have not tested CCP4MG on Catalina. I
>>> will install Catalina on one of my computers right away and see if I get
>>> the same problem. It may also depend on what graphics chip you have in your
>>> computer. We'll determine if that is important once I have upgraded.
>>>
>>> Best wishes,
>>> Stuart
>>>
>>> On Tue, 12 Nov 2019 at 20:44, Jerome Nwachukwu 
>>> wrote:
>>>
 Hi all,
 When I render images and try to save them, CCP4MG writes a status file,
 but does not save any image files.
 I have tried the two latest versions of CCP4MG. Could it be because I’m
 using macOS Catalina (version 10.15.1) ?


 

 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

>>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
> Dr Jon Agirre
> Royal Society University Research Fellow
> York Structural Biology Laboratory / Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
> http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
> Office: /B/K/065 Phone: +44 (0) 1904 32 8252
> Twitter: @glycojones
>



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Re: [ccp4bb] CCP4MG cannot save images in Mac OS

[Stuart McNicholas]

Dear Jerome,
   On my 13in Mid 2014 MacBook Pro with Intel Iris Graphics now running
Catalina (10.15.1), CCP4MG screenshots seem to work fine. What
Computer/Graphics chip are you using? I'll have to try upgrading a
different computer to see if I can reproduce the problem.

Best wishes,
Stuart


On Wed, 13 Nov 2019 at 08:56, Stuart McNicholas <
stuart.mcnicho...@york.ac.uk> wrote:

> Dear Jerome,
>It is entirely possible that this is a Catalina problem. I do not have
> a Catalina machine and hence have not tested CCP4MG on Catalina. I will
> install Catalina on one of my computers right away and see if I get the
> same problem. It may also depend on what graphics chip you have in your
> computer. We'll determine if that is important once I have upgraded.
>
> Best wishes,
> Stuart
>
> On Tue, 12 Nov 2019 at 20:44, Jerome Nwachukwu 
> wrote:
>
>> Hi all,
>> When I render images and try to save them, CCP4MG writes a status file,
>> but does not save any image files.
>> I have tried the two latest versions of CCP4MG. Could it be because I’m
>> using macOS Catalina (version 10.15.1) ?
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>



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[ccp4bb] ReNaFoBiS National School OLERON 2020

[CAVARELLI Jean (VIE)]

ReNaFoBiS. Oleron 2020. 

We are pleased to announce the 7th RéNaFoBiS Oléron workshop, dedicated to 
Integrative Structural Biology, that will take place on the Oléron island 
(France), from June the 12th until June the 19th, 2020. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, small 
angle X-ray scattering, NMR, cryo-electron microscopy, sample preparation for 
structural biology, biophysical methods to study and characterize 
macromolecular interactions). The goals are to explain and illustrate, to an 
audience mainly composed of doctoral students and young researchers, the 
contributions and limitations of each method with a strong emphasis on their 
complementarity/synergies and future developments. 
The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised. 
Registration will be open on a specific web site starting January 20th, 2020 
(maximum number of participants: 25). 
Applications will be evaluated upon deposition. 
More information on the French Initiative ReNaFoBiS : [ 
http://www.renafobis.fr/ | http://www.renafobis.fr/ ] 
Best regards 
Jean Cavarelli 
National ReNaFoBiS Coordinator 

 

ReNaFoBiS. 7eme École de Biologie Structurale Intégrative 
Oléron – du 12 au 19 juin 2020 

Le réseau RéNaFoBIS organise son école nationale du 12 au 19 juin 2020 à 
Oléron. Cette école propose une formation théorique et appliquée aux 
différentes approches utilisées en biologie structurale (diffraction et 
diffusion des rayons X, RMN, cryo-microscopie, préparations des échantillons en 
vue des études structurales, interactions macromoléculaires). Elle mettra 
l’accent sur l’intégration de plusieurs de ces méthodes pour répondre aux 
grandes questions de la biologie fonctionnelle à l’échelle atomique. 
Pour un public de doctorants ou de jeunes chercheurs, cette formation montrera 
les apports et les limites de chaque méthode et leur complémentarité. Elle 
inclura des sessions théoriques le matin et des travaux pratiques en groupes 
l’après-midi. 
Cette école est ouverte aux techniciens et ingénieurs (domaine académique et 
industriel) dans le cadre de la formation continue. Les conférences seront 
données principalement en français. Les supports des présentations seront en 
anglais, afin de permettre aux participants non-francophones de suivre plus 
facilement. Lors des sessions pratiques (TP), des groupes anglophones pourront 
être proposés si besoin. 
Le site Web spécifique d'inscriptions sera ouvert à partir du 20 janvier 2020 . 
Le nombre de places étant limité (25 participants), les participants seront 
sélectionnés sur la base d'un CV et d'une lettre de motivation. Les dossiers 
seront examinés et validés au fur et à mesure de leur déposition. 
Plus d'informations le site de ReNaFoBiS [ http://www.renafobis.fr/ | 
http://www.renafobis.fr/ ] 
Tres cordialement 
Jean Cavarelli 
Coordinateur National ReNaFoBiS 

- 
Jean Cavarelli 
Professor of Structural Biology 
"Structural biology of epigenetic targets" 
Department of Integrated structural biology 
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258 
phone : +33 (0)3 69 48 52 74 




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[ccp4bb] PhD positions in Synthetic and Structural Biology in the Max Planck Centre for Minimal Biology, Bristol UK

[kapil gupta]

Dear All,


We are looking for highly motivated and ambitious individuals to progress
our R programme on synthetic viral nanosystems (SVNs), to fill two PhD
posts available: one in next-generation vaccines and one in novel genome
engineering tools. The projects are in the frame of the BBSRC funded
doctoral training programme of the Sout West (SWBio DTP) and underpinned by
the European Research Council (ERC AdG DNA-DOCK) and the EPSRC Innovative
Vaccine Manufacturing and Research Hub.
The posts advertised synergistically combine complementary expertise in the
groups of Imre Berger (Max Planck Bristol Centre for Minimal
Biology), Christiane Schaffitzel (School of Biochemistry and Wellcome GW4
Cryo-EM Centre Bristol), Mark Dillingham (DNA Biology Unit, Bristol
University Bristol) and Frederic Garzoni from Imophoron SARL, an
award-winning vaccine innovator start-up at UnitDX Bristol.
   The projects follow from recent discoveries (e.g. Synthetic
self-assembling ADDomer platform for highly efficient vaccination by
genetically encoded multiepitope display, Science Advances, 2019; MultiBac:
Baculovirus-Mediated Multigene DNA Cargo Delivery in Insect and Mammalian
Cells, Viruses 2019; Highly efficient baculovirus-mediated multigene
delivery in primary cells. Nature Communications 2016) and aim to bring
about a step-change in the application of SVNs to combat infectious and
genetic disease.
The successful candidates should have a BSc, MSc or equivalent degree
in synthetic biology, molecular biology, protein biochemistry or related
fields and a strong interest in biodesign, protein engineering,
biochemistry and structural biology. We are looking for a creative and
ambitious person with good communication skills and keen to work on
challenging projects.

The Max Planck Center for Minimal Biology is a joint initiative of the
University of Bristol UK and the Max Planck Gesellschaft, Germany. The
groups involved use synthetic biology, protein engineering, *in vitro*
selection/evolution, cryo-electron microscopy, x-ray crystallography) to
create new vaccines and advanced genome engineering tools.

The groups at Bristol have excellent access to state-of-the-art
synthetic biology technologies including platforms for in vitro
selection/evolution (Ribosome Display) and protein production (MultiBac).
The in house EM facility is  equipped with a microscopes including an
Arctica/K2. Additionally, we have access to the Titan Krios microscopes and
the X-ray beamlines at the nearby National Facility at Diamond/Harwell. Other
facilities on the Bristol campus include microfluidics, high performance
computing, high-field NMR and  high-throughput crystallization
Biosuite, mammalian
facilities, biophysical platform and confocal microscopy in the Bristol
BioSuite and Wolfson facilities.

Interested and excited? You can find out more about these vacancies here:

https://www.linkedin.com/posts/imre-berger-7a0a6a50_addomer-synthetic-multiepitope-virus-like-activity-6595367002435649536-anJV

https://www.linkedin.com/feed/update/urn:li:activity:6598170469470355456/

or by contacting Imre Berger: imre.ber...@bristol.ac.uk

or Christiane Schaffitzel: christiane.berger-schaffit...@bristol.ac.uk


Please apply online through:

https://www.findaphd.com/phds/project/addomer-synthetic-multiepitope-virus-like-particle-platform-for-next-generation-vaccines/?p108225https://www.findaphd.com/phds/project/precision-genome-editing-using-modulators-of-dsdna-break-repair-pathways/?p114537


Kapil Gupta on behalf of

Prof. Imre Berger PhD HDR FRSB

Founding Director, Max Planck Centre for Minimal Biology

Chair in Biochemistry and University Research Fellow
Wellcome Trust Senior Investigator, ERC Investigator

Co-Director, Bristol Biodesign Institute BBI

Director, BrisSynBio Centre


School of Biochemistry,  Faculty of Life Sciences and

Max Planck Bristol Centre for Minimal Biology and

BrisSynBio, an EPSRC/BBSRC Centre for Synthetic Biology

University of Bristol

1 Tankard's Close

Bristol  BS8 1TD

Tel: 0044 (0) 117 39 41857
Mobile: 0044 (0) 79 0720 8697


maxplanck-minimalbiology.bristol.ac.uk/




www.bris.ac.uk/biomedical-sciences/ 

www.bristol.ac.uk/research/institutes/biodesign/

www.bristol.ac.uk/brissynbio



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Re: [ccp4bb] CCP4MG cannot save images in Mac OS

[Stuart McNicholas]

Dear Jerome,
   It is entirely possible that this is a Catalina problem. I do not have a
Catalina machine and hence have not tested CCP4MG on Catalina. I will
install Catalina on one of my computers right away and see if I get the
same problem. It may also depend on what graphics chip you have in your
computer. We'll determine if that is important once I have upgraded.

Best wishes,
Stuart

On Tue, 12 Nov 2019 at 20:44, Jerome Nwachukwu  wrote:

> Hi all,
> When I render images and try to save them, CCP4MG writes a status file,
> but does not save any image files.
> I have tried the two latest versions of CCP4MG. Could it be because I’m
> using macOS Catalina (version 10.15.1) ?
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] PostDoc position at EMBL Grenoble to work on ESRF beamline MASSIF-1

[Matthew Bowler]

Dear All,

we have a post-Doc position available here at EMBL Grenoble shared 
between the high throughput crystallisation team 
(https://www.embl.fr/services/ht_crystallisation/index.html) and the 
synchrotron team (https://www.embl.fr/research/unit/mccarthy/index.html) 
to work with me on ESRF beamline MASSIF-1 (http://www.esrf.eu/MASSIF1). 
MASSIF-1 has pioneered fully automated data collection, including sample 
location and decision making algorithms (see 
https://doi.org/10.1107/S2059798318003728 
http://dx.doi.org/10.1107/S1399004715011918 
http://dx.doi.org/10.1107/S1600577515016604) Next year will see two 
exciting upgrades to the beamline - first, the ESRF will be coming back 
on-line after completely re-building the accelerator 
(https://www.esrf.eu/about/upgrade) as the worlds first fourth 
generation synchrotron - ESRF-EBS - we will be upgrading the beamline 
optics to maximise the capabilities of the new source. Second, the 
experimental station of MASSIF-1 will be completely refurbished to have 
a new diffractometer and the revolutionary sample mounting robot, 
CrystalDirect (http://dx.doi.org/10.1107/s2059798316000954 
http://dx.doi.org/10.1107/s0907444912031459) will also be installed on 
the beamline bringing automation all the way from pure protein to 
structure models (see http://dx.doi.org/10.1063/1.5084627)


This is an exciting opportunity  to be involved in the commissioning of 
an MX beamline at the forefront of automation. This will be a highly 
collaborative position working with the EMBL instrumentation, HTX and 
synchrotron teams as well as the ESRF towards the design, construction 
and operation of the upgraded MASSIF-1 beamline with a focus on 
expanding its capabilities to support automated fragment screening and 
crystallography pipelines. You will also contribute towards the 
development of new methods exploiting the unique experimental 
opportunities provided by the integration of the CrystalDirect 
technology in a beamline environment. You will also participate in 
research projects involving fragment screening and development of 
chemical tools on targets of biomedical relevance.


Please feel free to contact me, Josan Marquez (marq...@embl.fr) or 
Andrew McCarthy (andre...@embl.fr) for informal inquiries - you will 
need to apply here 
https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00140=1[]=4 
Closing date is the 15th December and interviews will be 27th January 2020.


Best wishes, Matthew.

--
Matthew Bowler
Synchrotron Crystallography Group
European Molecular Biology Laboratory
71 avenue des Martyrs
CS 90181 F-38042 Grenoble
France
===
Tel: +33 (0) 4.76.20.76.37
Fax: +33 (0) 4.76.20.71.99

http://www.embl.fr/
http://www.esrf.eu/MASSIF1
https://twitter.com/id30_massif1
http://www.embl.fr/research/unit/mccarthy/members/index.php?s_personId=CP-60015559
===



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