[ccp4bb] Senior Scientist (M/F) in Protein Crystallography at ZoBio

[Willem-Jan Waterreus]

Dear community,

ZoBio is looking for a senior protein crystallographer (M/F) with experience in 
drug design. The ideal applicant has a demonstrable track record solving 
protein-ligand structures and has worked with medicinal chemists to interpret 
these results for drug discovery campaigns. The candidate should have a clear 
vision on how crystallography should be integrated into the wider small 
molecule drug discovery process and take the initiative to put this into 
practice.

ZoBio is a privately held, self-funded, successful and growing company that was 
spun out of Leiden University (Leiden, The Netherlands) in 2004. We are a 
contract research organization that offers research services in the field of 
small molecule drug discovery. We are also a leading innovator in developing an 
array of protein engineering and biophysical techniques to support hit-to-lead 
programs in the pharmaceutical industry. We are a dynamic, science driven team 
whose vision is to deliver the ultimate in value to our clients.

For further particulars and to apply for this post, please follow: 
http://www.zobio.com/senior-scientist-mf-in-protein-crystallography-fulltime/

Best regards,

Willem-Jan Waterreus

[ccp4bb] Scientific programmer - EM Validation

[Ardan Patwardhan]

Dear all

Just a note that the deadline to apply for this position is Sunday the 10th of 
December 2017:

I am looking for a person with a structural biology/bioinformatics background 
and software development experience to work on an exciting joint project with 
Garib Murshudov’s group (MRC-LMB) to develop structural data-mining of 3DEM 
maps in EMDB with the aim of deriving canonical 3D density motifs that can be 
used for validation and analysis.

More details can be found here: 
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01074 


Many thanks and best wishes


Ardan Patwardhan
Team Leader - Cellular Structure & 3D Bioimaging
EMDB & EMPIAR
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology 
Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Tel: +44 1223 492649

Re: [ccp4bb] XQuartz and High Sierra OSX

[Steiner, Roberto]

Yes. Things are now fine using 2.7.11. I just had to play a bit with the Apple 
Thunderbolt Display which was causing XQuartz to behave funny.
Problem solved.

Cheers
Roberto


On 4 Dec 2017, at 13:39, Engin Özkan 
mailto:eoz...@uchicago.edu>> wrote:


Hi,

I have been using Xquartz 2.7.11 (the latest release) perfectly fine on High 
Sierra. We did not have to downgrade to 2.7.8. CCP4i and Coot works perfectly 
fine with XQuartz 2.7.11 on multiple iMacs and MacBook Pros we have in the lab.

Best,

Engin

On 12/4/17 4:49 AM, Martin Montgomery wrote:
Dear Roberto,

You can install Xquartz 2.7.8 which is still available from the xquartz web 
site.  This was the last version where Xquartz behaved properly and it runs 
fine on High Sierra.

Regards

MGM


Martin G Montgomery
Medical Research Council Mitochondrial Biology Unit
University of Cambridge
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk

On 2 Dec 2017, at 00:04, Steiner, Roberto 
mailto:roberto.stei...@kcl.ac.uk>> wrote:

Hi all

Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - 
fresh installation) does not longer behave properly. Essentially, X11 does not 
seem to understand touchpad actions (for example cannot close X11 windows, 
cannot drag them around, etc.). This problems also affects programs that rely 
on X11. Has anyone experienced (and ideally solved) this problem?

Thanks in advance
Roberto

Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London




Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Re: [ccp4bb] XQuartz and High Sierra OSX

[Engin Özkan]

Hi,

I have been using Xquartz 2.7.11 (the latest release) perfectly fine on 
High Sierra. We did not have to downgrade to 2.7.8. CCP4i and Coot works 
perfectly fine with XQuartz 2.7.11 on multiple iMacs and MacBook Pros we 
have in the lab.


Best,

Engin


On 12/4/17 4:49 AM, Martin Montgomery wrote:

Dear Roberto,

You can install Xquartz 2.7.8 which is still available from the 
xquartz web site.  This was the last version where Xquartz behaved 
properly and it runs fine on High Sierra.


Regards

MGM


Martin G Montgomery
Medical Research Council Mitochondrial Biology Unit
University of Cambridge
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk 

On 2 Dec 2017, at 00:04, Steiner, Roberto > wrote:


Hi all

Since my recent upgrade to High Sierra, XQuartz (most recent version 
2.7.11 - fresh installation) does not longer behave properly. 
Essentially, X11 does not seem to understand touchpad actions (for 
example cannot close X11 windows, cannot drag them around, etc.). 
This problems also affects programs that rely on X11. Has anyone 
experienced (and ideally solved) this problem?


Thanks in advance
Roberto

Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk 
Phone 0044 20 78488216
Fax    0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

[ccp4bb] ccp4 release 7.0 update 047

[Charles Ballard]

Dear All

update 047 is out and contains

* mmdb2
- fix for false duplicate sequence number error in case of short residue names

* panddas
- version 2.11.0

* edstats
- new version

* ccp4i2
- updates to molrep interface

* pointless
- 1.115, bug fix for multi-lattice data

* lorestr
- fix to ccp4i interface

* molrep
- fix in PFmod

* ccp4mg
- fix in MG/MrBUMP alignment
- update download from PDBe

* monomers
- add 0WD,2Q5,6G6,6ZL,79F,7K9,8LL,9Q8,FJI,OMZ,QUJ,QVE,RU2,YY9
- fix CPN,CPO,DEF,GCR,IMF,QPT
- replace UAP


CCP4 Core Team

Next update DIALS 1.8.1, auspex plus various bug fixes

Re: [ccp4bb] XQuartz and High Sierra OSX

[Martin Montgomery]

Dear Roberto,

You can install Xquartz 2.7.8 which is still available from the xquartz web 
site.  This was the last version where Xquartz behaved properly and it runs 
fine on High Sierra.

Regards

MGM


Martin G Montgomery
Medical Research Council Mitochondrial Biology Unit
University of Cambridge
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road 
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk

> On 2 Dec 2017, at 00:04, Steiner, Roberto  wrote:
> 
> Hi all
> 
> Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - 
> fresh installation) does not longer behave properly. Essentially, X11 does 
> not seem to understand touchpad actions (for example cannot close X11 
> windows, cannot drag them around, etc.). This problems also affects programs 
> that rely on X11. Has anyone experienced (and ideally solved) this problem? 
> 
> Thanks in advance 
> Roberto
> 
> Roberto A. Steiner, PhD
> Randall Centre of Cell and Molecular Biophysics
> Faculty of Life Sciences and Medicine 
> King's College London
> 
> roberto.stei...@kcl.ac.uk 
> Phone 0044 20 78488216
> Fax0044 20 78486435
> 
> Room 3.10A
> New Hunt's House
> Guy's Campus
> SE1 1UL
> London
> 

Re: [ccp4bb] XQuartz and High Sierra OSX

[Steiner, Roberto]

Solution: I noticed yesterday that XQuartz was behaving normally when my laptop 
was not connected to the Apple Thunderbolt Display. Resetting the Thunderbolt 
Display solved the problem.

Roberto

On 2 Dec 2017, at 00:04, Steiner, Roberto 
mailto:roberto.stei...@kcl.ac.uk>> wrote:

Hi all

Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - 
fresh installation) does not longer behave properly. Essentially, X11 does not 
seem to understand touchpad actions (for example cannot close X11 windows, 
cannot drag them around, etc.). This problems also affects programs that rely 
on X11. Has anyone experienced (and ideally solved) this problem?

Thanks in advance
Roberto

Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London



Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Re: [ccp4bb] new ContaMiner features

[Marcin Wojdyr]

On 2 December 2017 at 00:31, Ivan Shabalin
 wrote:

>  Instead, we just used the search of the
> unit cell parameters in the PDB, which is much faster (but works only if the
> structure of this particular artifact in the same SpGr is in PDB! otherwise,
> one should use ContaMiner or similar service). This feature is implemented
> in HKL3000, but it can also be done quickly on the PDB webpage.

Even better, one can use SAUC which finds also matches in different
space groups by comparing dimensions of the Niggli (reduced) cell.
http://iterate.sourceforge.net/sauc/