Re: [ccp4bb] Refmac automatically handles twinning?

2022-03-30 Thread Eleanor Dodson 
I am sure you have checked this but
A) is there non cryst translation? If so this can make space group
selection tricky . Could it be P3  21 or P31 21 or ...
B ) the twin indicators at data processing are pretty reliable and if that
suggests no twinning it probably isn’t there... you could process bits
separately to see if bens idea is likely.

C) I see data sets where long runs if vatches are totally wrong - Rmerge >1
etc - no idea why but you need to cut them out of the data processing

All very puzzling!
Eleanor

On Thu, 31 Mar 2022 at 05:46, Ben Bax  wrote:

> The twin fraction can vary during data collection - if the beam is smaller
> than the crystal
> For example you could have crystals which are like two very short ends of
> pencils - with flat ends together (in your case these might pencils could
> be in P3)
> In some orientations you could have the beam going through only one pencil
> (not twinned) and some orientations going through both pencils ( 50:50
> twin).
> This is not yet properly handled in the data processing.
>
>
>
> On 29 Mar 2022, at 09:39, Nicholas Keep  wrote:
>
> Just double checking that Refmac automatically handles twinning without
> the need for a keyword or a box click in i2.  I have a crystal in P32 21
> that gives poor Rfactors and maps (Rfree mid 40s) from what should be an
> excellent model. I have reprocessed in P32, P1 and C2 but all give similar
> results so it appears not to be hidden twinning.  There is no need to click
> a box or enter a keyword for this to be a check for twinning ?
>
> There is severe anisotropy and a few other problems flagged up in iSPYB so
> there may be more complex problems than twinning with these crystals
>
> Best wishes
>
> Nick
>
> --
> Prof Nicholas H. Keep
> Emeritus Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> Dept email n.k...@bbk.ac.uk
> Telephone 020-3926-3475  (Will contact me at home if working as well as my
> office)
>
> 
>
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Re: [ccp4bb] Refmac automatically handles twinning?

2022-03-30 Thread Ben Bax 
The twin fraction can vary during data collection - if the beam is smaller than 
the crystal
For example you could have crystals which are like two very short ends of 
pencils - with flat ends together (in your case these might pencils could be in 
P3)
In some orientations you could have the beam going through only one pencil (not 
twinned) and some orientations going through both pencils ( 50:50 twin).
This is not yet properly handled in the data processing.



On 29 Mar 2022, at 09:39, Nicholas Keep  wrote:

Just double checking that Refmac automatically handles twinning without the 
need for a keyword or a box click in i2.  I have a crystal in P32 21 that gives 
poor Rfactors and maps (Rfree mid 40s) from what should be an excellent model. 
I have reprocessed in P32, P1 and C2 but all give similar results so it appears 
not to be hidden twinning.  There is no need to click a box or enter a keyword 
for this to be a check for twinning ?

There is severe anisotropy and a few other problems flagged up in iSPYB so 
there may be more complex problems than twinning with these crystals

Best wishes

Nick

-- 
Prof Nicholas H. Keep
Emeritus Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Dept email n.k...@bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)



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[ccp4bb] Beam time available now at MacCHESS

2022-03-30 Thread Doletha Marian Szebenyi 



From: Doletha Marian Szebenyi 
Sent: Wednesday, April 14, 2021 10:12 AM
To: ccp4bb@jiscmail.ac.uk 
Subject: Beam time available now at MacCHESS


Rapid access beam time for macromolecular crystallography is available now at:
[cid:324d0976-5c56-4ddf-884f-4ec63b50ac92]
Features include:

  *   EIGER2 16M detector
  *   Automounter accepting MSC pucks, Unipucks, Rigaku pucks (loaner kit with 
MSC pucks available)
  *   100 µ standard beam or 15 µ minibeam (focused with CRL)
  *   Full 24-hr support for remote or in-person operation
  *   Cryo or room-temperature data collection
  *   High-pressure cryocooling option to improve diffraction quality or trap 
gases
  *   Serial crystallography option (fixed-target)
  *   High-pressure data collection in diamond anvil cell

Visit the CHESS User Portal to request beam 
time. For more information, visit our web 
site or contact me (dm...@cornell.edu).

Marian Szebenyi
Director, MacCHESS



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[ccp4bb] Postdoctoral position at the Institute for Structural Biology, Grenoble

2022-03-30 Thread Malene Ringkjobing Jensen 
Postdoctoral position on scaffold protein assemblies in MAPK cell signalling

A 2-year postdoctoral position (with possible extension) is available from the 
1st of June 2022 in the team of Dr. Malene R. Jensen at the Institute for 
Structural Biology (IBS) in Grenoble, France. The successful candidate will 
work on the structure and dynamics of scaffold proteins and study their 
interactions with kinases of the mitogen-activated protein kinase (MAPK) cell 
signalling pathways. We exploit a combination of X-ray crystallography and NMR 
spectroscopy. 

More information can be found on the team website: www.jensen-nmr.fr 


Facilities
The Institute for Structural Biology  is 
located on the EPN science campus in Grenoble in close proximity to the 
European Synchrotron Radiation Facility (ESRF), the European Molecular Biology 
Laboratory (EMBL) Grenoble Outstation and the Institute Laue-Langevin (ILL). 
The IBS houses six high-field NMR spectrometers (3 x 600, 700, 850 and 950 MHz) 
and wetlab facilities for cloning, expression and purification of proteins. 
Access is facilitated to a number of state-of-the-art research platforms 
through Integrated Structural Biology Grenoble .

Qualifications
The ideal candidate holds a PhD in chemistry, biochemistry or biophysics (or 
related discipline) and has experience in protein expression and purification 
and a proven track-record in solution NMR spectroscopy and/or X-ray 
crystallography. To apply for this position, please send your CV, a motivation 
letter and the names of two referees to malene.ringkjobing-jen...@ibs.fr 


Recent relevant publications

L. Mariño Pérez, F.S. Ielasi, L.M. Bessa, D. Maurin, J. Kragelj, M. Blackledge, 
N. Salvi, G. Bouvignies, A. Palencia, M.R. Jensen
Nature (2022), 602, 695-700. 

Visualizing protein breathing motions associated with aromatic ring flipping

K.K. Rasmussen, A. Palencia, A.K. Varming, H. El-Wali, E. Boeri Erba, M. 
Blackledge, K. Hammer, T. Herrmann, M. Kilstrup, L. Lo Leggio, M.R. Jensen
Proc. Natl. Acad. Sci. U.S.A. (2020) 117, 20576-20585. 

Revealing the mechanism of repressor inactivation during switching of a 
temperate bacteriophage

E. Delaforge, J. Kragelj, L. Tengo, A. Palencia, S. Milles, G. Bouvignies, N. 
Salvi, M. Blackledge, M.R. Jensen
J. Am. Chem. Soc. (2018) 140, 1148-1158. 

Deciphering the dynamic interaction profile of an intrinsically disordered 
protein by NMR exchange spectroscopy

J. Kragelj, A. Palencia, M. Nanao, D. Maurin, G. Bouvignies, M. Blackledge, 
M.R. Jensen
Proc. Natl. Acad. Sci. (2015) 112, 3409-3414. 

Structure and dynamics of the MKK7-JNK signalling complex


-- 
Dr. Malene Ringkjøbing Jensen
Research Director CNRS
Institut de Biologie Structurale
71, avenue des Martyrs
CS 10090
38044 Grenoble CEDEX 9
France


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