[ccp4bb] Postdoctoral position at the Institute of Structural and Molecular Biology, London, UK

[Philip JJ Robinson]

I would like make you aware of an opening for a postdoctoral  
researcher in the Robinson Lab at the Institute of Structural and  
Molecular Biology (ISMB) within Birkbeck College, London UK. We are  
seeking an ambitious and driven research scientist to investigate the  
structure and function of a biomedically important family of chromatin  
modifying complexes.


The position will involve interdisciplinary research combining  
biophysical and structural approaches (X-ray crystallography and  
cryo-EM) and features exciting collaborative opportunities with groups  
at UCSF and the Institut Pasteur. The qualified candidate should have  
obtained a Ph.D. with a solid foundation in biophysical approaches and  
experience in biochemistry and structural biology.


The ISMB is a vibrant, multidisciplinary and collaborative research  
environment that bridges the Departments of Chemistry/Structural and  
Molecular Biology at University College London and the Department of  
Biological Sciences at Birkbeck. The ISMB is a UK centre of excellence  
for cryo-electron microscopy and X-ray crystallography. The EM suite  
currently houses a 300KeV Polara with K2 detector as well as FEI  
Tecnai F20, T12 and T10 for sample characterization and optimization.  
Cryo-EM capabilities will be further strengthened by a recently  
purchased 300KeV FEI Titan Krios, to be delivered in early 2018. The  
X-ray lab comprises a robotics suite for liquid handling, tray setup,  
barcoding and imaging and an X-ray room for in-house diffraction  
experiments.


The full-time post is funded by the Medical Research Council for a  
period of up to five years, includes a competitive London-weighted  
salary and will be available from May 2018. For more information about  
the position and to apply, use the following link:


http://jobs.bbk.ac.uk/fe/tpl_birkbeckcollege01.asp?s=4A515F4E5A565B1A=66121,8848474812=118857330=35481286468798=sebepmfuvkhzehsxxn

Informal enquiries are welcome and can made via email to Dr Philip  
Robinson (p.robin...@mail.cryst.bbk.ac.uk).



Philip Robinson Ph.D
MRC CDA Fellow and Group Leader
Institute of Structural and Molecular Biology
Department of Biological Sciences
Birkbeck, University of London
Malet Street, London WC1E 7HX
United Kingdom

[ccp4bb] Postdoctoral position in Melbourne, Walter and Eliza Hall Institute, Australia

[Isabelle Lucet]

Postdoctoral position, Walter and Eliza Hall Institute of Medical Research.

If you are interested in understanding the intricacy of Kinases/Pseudokinases 
regulation using CryoEM, X-ray crystallography, Imaging and chemical biology 
approaches,  we have an exciting opportunity for a postdoctoral position at the 
Walter and Eliza Hall Institute of Medical Research, reporting to Dr Isabelle 
Lucet.

The position is offered for one year in the first instance.
Check out the full details on:
https://www.wehi.edu.au/research-officer-lucet-laboratory

Closing date: 28 February 2018
Contact email:luce...@wehi.edu.au

---
Isabelle Lucet, PhD
Laboratory Head
ACRF Chemical Biology Division

The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia

Phone +61 3 9345 2873 |
Email: luce...@wehi.edu.au Web 
http://www.wehi.edu.au

The ACRF Chemical Biology Division is supported by the

[cid:38C5DB05-C184-460B-AE9C-55AA19A1DEB9]

Re: [ccp4bb] Arg distorsion during refinement

[Dale Tronrud]

   Coincidentally, I just noticed this problem while perusing a
validation report last night and am tooling up to see if I can get this
problem fixed.

   The origin of the flaw is the asymmetry of the NH1 and NH2 atoms in
Arginine.  If one considers only bonding it would appear that these two
atoms are interchangeable, but one clashes with CD and the other does
not.  The clash causes one bond angle to be larger than 120 deg and the
other to be smaller.  To allow this situation to be described the IUPAC
convention says that the atom near CD should be named NH1 and the other
one name NH2.  This naming convention is one of the things that Coot
begs to be allowed to fix every time you start it.

   In the Engh & Huber library (2001) this convention was not imposed
and their analysis was performed with the assumption that these two
angles are equivalent.  The result is a symmetrized value midway between
the two correct values, which as you note are about 123 deg and 117 deg.

   The bundling together of these two angles shouldn't cause a
validation problem expect for the fact the Engh & Huber assigned the
impossibly small sigma of 0.5 deg to this angle.  A 50/50 mixture of
angles each centered on 123 and 117 should have a sigma upwards of six
degrees.  Such a sigma would give a pass to correct models, but a 0.5
deg sigma will flag correct models with 6 sigma deviations.

   Until we can get the validation report generator fixed you should
tell this story to anyone who complains about your model.  Your model is
fine and the validation software needs better validation itself.

Dale Tronrud


On 2/9/2018 10:18 AM, Oganesyan, Vaheh wrote:
> Dear crystallographers,
> 
>  
> 
> Lately when refining a structure (at 2.8A) with Refmac5 I’ve found that
> nearly all Arg residues get distorted at one angle:  NE-CZ-NH1(2).
> Starting model has 120°, final model 123°(117°), which validation server
> considers a major issue. May any of you recognize why is this happening?
> Don’t remember seeing anything like this before.
> 
> Current CCP4 version 7.0.050; Refmac5 version 5.8.0189.
> 
>  
> 
> Last structure deposited in December’17 did not have those issues. CCP4
> version then was 7.0.047; Refmac5 version was the same.
> 
>  
> 
> Thank you for your time.
> 
>  
> 
> Regards,
> 
>  
> 
> /Vaheh Oganesyan/
> 
> /MedImmune, ADPE/
> 
> /www.medimmune.com/
> 
>  
> 
>  
> 
> To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information
> is considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by the
> individual(s) for whom it is intended. If you have received this
> electronic communication in error, please reply to the sender advising
> of the error in transmission and delete the original message and any
> accompanying documents from your system immediately, without copying,
> reviewing or otherwise using them for any purpose. Thank you for your
> cooperation.

Re: [ccp4bb] Confidential Validation report

[Bernhard Rupp]

I strongly recommend doing a full validation and error check with the 
validation server 

 

https://validate-rcsb-1.wwpdb.org/

 

*BEFORE* you submit the actual deposition for annotation.

Due to various shortcomings of the deposition software (e.g. the old validation 
report remaining in the validation pages

despite you fixed the errors) it is a total pain for both, the depositor and 
the annotators, to fix things after the annotation.

 

Best, BR 

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of abhimanyu 
singh
Sent: Friday, February 9, 2018 2:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Confidential Validation report

 

Hi Jinyu,

 

You will get the full validation reports once the entries are annotated by the 
PDB and you will be notified. The reports can then be accessed after logging 
into the respective deposition sessions.

 

 

Greetings,

Abhi

 

 

On Fri, 9 Feb 2018 at 21:53 jlliu20022002 liu  > wrote:

Hi All, I have not deposited structures for a while and hope to get some 
information from here. I recently deposited 2 structures. I got the preliminary 
validation report and is still in communication with pdb staff regarding 
details of the deposition. My question is when I would be able to get the” 
confidential validation report” . I am waiting for these reports to submit the 
paper?  Thanks a lot in advice for your inputs.

 

Jinyu

-- 

Abhimanyu Kumar Singh, PhD
Post-doctoral Research Associate

School of Biosciences

University of Kent

Canterbury CT2 7NJ, UK.

a.k.si...@kent.ac.uk   

  abhimanyu.si...@cnb.csic.es

http://www.pde4npd.eu/

Re: [ccp4bb] Confidential Validation report

[abhimanyu singh]

Hi Jinyu,

You will get the full validation reports once the entries are annotated by
the PDB and you will be notified. The reports can then be accessed after
logging into the respective deposition sessions.


Greetings,
Abhi


On Fri, 9 Feb 2018 at 21:53 jlliu20022002 liu 
wrote:

> Hi All, I have not deposited structures for a while and hope to get some
> information from here. I recently deposited 2 structures. I got the
> preliminary validation report and is still in communication with pdb staff
> regarding details of the deposition. My question is when I would be able to
> get the” confidential validation report” . I am waiting for these reports
> to submit the paper?  Thanks a lot in advice for your inputs.
>
> Jinyu
>
-- 
*Abhimanyu Kumar Singh, PhD*
Post-doctoral Research Associate
School of Biosciences
University of Kent
Canterbury CT2 7NJ, UK.
a.k.si...@kent.ac.uk
abhimanyu.si...@cnb.csic.es
http://www.pde4npd.eu/

[ccp4bb] Confidential Validation report

[jlliu20022002 liu]

Hi All, I have not deposited structures for a while and hope to get some
information from here. I recently deposited 2 structures. I got the
preliminary validation report and is still in communication with pdb staff
regarding details of the deposition. My question is when I would be able to
get the” confidential validation report” . I am waiting for these reports
to submit the paper?  Thanks a lot in advice for your inputs.

Jinyu

[ccp4bb] Arg distorsion during refinement

[Oganesyan, Vaheh]

Dear crystallographers,

Lately when refining a structure (at 2.8A) with Refmac5 I've found that nearly 
all Arg residues get distorted at one angle:  NE-CZ-NH1(2). Starting model has 
120*, final model 123*(117*), which validation server considers a major issue. 
May any of you recognize why is this happening? Don't remember seeing anything 
like this before.
Current CCP4 version 7.0.050; Refmac5 version 5.8.0189.

Last structure deposited in December'17 did not have those issues. CCP4 version 
then was 7.0.047; Refmac5 version was the same.

Thank you for your time.

Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com


To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
reviewing or otherwise using them for any purpose. Thank you for your 
cooperation.

[ccp4bb] Postbaccalaureate position in membrane protein structure and function at the NIH

[Anirban Banerjee]

Dear all,

>
> I am looking for a postbac for a membrane protein
> structure-function project in my lab at the NIH. We are currently focusing
> on integral membrane enzymes (Science. 2018,  doi:
> 10.1126/science.aao6326) and transporters of transition metal ions (J
> Biol Chem. 2018, doi: 10.1074/jbc.M117.817478). The NIH Postbac IRTA
> program provides recent college graduates who are planning to apply to
> graduate or professional (medical/dental/pharmacy) school an opportunity to
> spend one or two years performing full-time research at the NIH.
>

> For this position I am looking for someone who has experience with protein
> purification, has good organizational skills and work ethics, and the right
> mindset to pay attention to nitty-gritty details that are essential for
> working with membrane proteins. The candidate should apply to the NIH
> Postbac Program (https://www.training.nih.gov/programs/postbac_irta)  and
> get in touch with me as well.
>
> Postbac candidates have to be US citizens or permanent residents.
>
> Thanks very much.
>

Anirban Banerjee

Re: [ccp4bb] Might be of interest to this group

[Keller, Jacob]

I hope everyone realizes that I am very happy with off-topics, and love the 
praying mantis thing. It didn’t come off as cynical, did it? I just thought it 
funny to post to the crystallography list, and somewhat humorous to picture 
praying mantises running COOT etc.

We should really find an organism which sees in reciprocal space, figure out 
how it solves the phase problem, then implement it in software. Or train 
ourselves to do it by wearing Fourier glasses—then we could just do all of our 
modelling in reciprocal space, save a lot of time.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

Re: [ccp4bb] Might be of interest to this group

[Keller, Jacob]

Or for the Praying Mantis Crystallographers’ association?

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andreas 
Forster
Sent: Friday, February 9, 2018 11:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Might be of interest to this group

Wouldn’t that be something for the PyMOL mailing list?

All best - Andreas
On Fri, 9 Feb 2018 at 20:38, David Schuller 
> wrote:

http://www.cell.com/current-biology/fulltext/S0960-9822(18)30014-9

A Novel Form of Stereo Vision in the Praying Mantis
Vivek Nityananda,Ghaith Tarawneh, Sid Henriksen,Diana Umeton,Adam Simmons, 
Jenny C.A. Read

DOI: https://doi.org/10.1016/j.cub.2018.01.012

Current Biology

--

===

All Things Serve the Beam

===

   David J. Schuller

   modern man in a post-modern world

   MacCHESS, Cornell University

   schul...@cornell.edu

Re: [ccp4bb] Postdoc position, structural biology, University of Cambridge, UK

[Prof.V Koronakis]

> 
> Dear structural biologists,
> 
> We have an opportunity for a postdoctoral researcher in my lab in the 
> School of Biological Sciences, Department of Pathology, University of 
> Cambridge, UK. The successful applicant will continue our work on  
> bacterial multidrug resistance pumps, (e.g. see our recent PNAS paper 
> here (http://www.pnas.org/content/114/47/12572.full 
> ) and other medically 
> important membrane machineries.
> 
> We're looking for someone with a PhD in structural 
> biology/biochemistry/biophysics and demonstrable experience in X-ray 
> crystallography 
> and/or cryoEM. Funds are available until August 2020 in the first instance.
> Full job description is here, along with details of how to apply through the 
> University jobs portal:
> http://www.jobs.cam.ac.uk/job/16385/  
> 
> Best wishes,
> 
> Vassilis Koronakis
> 
> Dr Vassilis Koronakis
> Professor of Molecular Biology
> Wellcome Trust Senior Investigator
> University of Cambridge
> Department of Pathology
> Tennis Court Road Cambridge CB2 1QP
> 
> 
> 

Re: [ccp4bb] Might be of interest to this group

[Andreas Forster]

Wouldn’t that be something for the PyMOL mailing list?

All best - Andreas
On Fri, 9 Feb 2018 at 20:38, David Schuller  wrote:

> http://www.cell.com/current-biology/fulltext/S0960-9822(18)30014-9
> A Novel Form of Stereo Vision in the Praying Mantis
> Vivek Nityananda ,Ghaith Tarawneh, Sid
> Henriksen,Diana Umeton,Adam Simmons, Jenny C.A. Read
>
> DOI: https://doi.org/10.1016/j.cub.2018.01.012
>
> Current Biology
>
> --
> ===
> All Things Serve the Beam
> ===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>schul...@cornell.edu
>
>

[ccp4bb] ACA 2018 - Small Angle Scattering Workshop

[Kushol Gupta]

 

 

 








 





"Applications of Small Angle Scattering to Structural Biology: An
Introduction." 









On behalf of the organizing committee, we are pleased to announce a workshop
on "Applications of Small Angle Scattering to Structural Biology: An
Introduction." 


This workshop will take place on Friday, July 20th, 2018 at this year's
American Crystallographic Association (ACA) Meeting in Toronto, Canada. The
meeting itself will run from July 20-24.
 
Over the past two decades, SAS has become a mainstay technique for the study
of structure and composition in solution for structural biologists around
the world. In contrast to the more intensive SAS courses in Europe that
extend across several days, this single-day workshop will be comprised of
carefully constructed lectures and tutorials to serve as an introduction to
investigators new to the technique. The workshop format will include
lectures and a selection of hands-on practical exercises.  Throughout the
workshop the emphasis will be on practical application: knowing how to judge
data quality, how to troubleshoot during data collection, and the
expectations for a successful experiment and acceptable publication.
Students will also learn about aspects of home laboratory data collection
and will be introduced to experiments at national user facilities
(synchrotrons and research reactors).   
 
Students will be expected to bring laptops with the appropriate
pre-installed software. Extra laptops will be provided in case of unexpected
hardware or software issues on-site, and network connectivity will be
provided as part of the course, as some exercises and tutorials will reply
on external computer-server resources. Preloaded portable disks and memory
sticks will be provided to help reduce the need for large downloads over
conference bandwidth.
 
We thank Anton-Paar, Rigaku Corporation, SAXSLAB, and Wyatt Technology
Corporation for their kind support of this event.
 
Tentative Program Schedule
 


Time

Topic


8:00 AM

Registration and Software Installation Help; Speaker Introduction


8:30 AM

BioSAS: Overview 
Why is SAS helpful?


9:00 AM

The Scattering Profile 
Guinier analysis, concentration, monodispersity, etc.


9:30 AM

Tutorial 1: Basic Data Analysis I with RAW 
Is this good data? Radiation Damage?


10:00 AM

Coffee Break


10:15 AM

Data Analysis: Model-independent Features 
Molecular Weight Determination, Invariant Plots and Flexibility, The P(r)
function


11:00 AM

Tutorial 2: Basic Data Analysis II with RAW 
Calculate a P(r) function, determine Molecular Weight, Dmax, Rg, Volume,
etc.


12:00 PM

Working Lunch - Laboratory Source SAXS 
Discussion with Scientists, Experimental Advice


1:00 PM

SEC-SAXS 
Application and Practical Considerations


1:30 PM

Sample Preparation
Sample purification and preparation, aggregation, buffer selection, etc


1:45 PM

Complementary Biophysical Methods for Sample Assessment 
The importance of supporting biophysical methods including static and
dynamic light scattering and analytical ultracentrifugation  


2:00 PM

Data Analysis: Model-dependent Analysis of SAS Data
Calculated scattering profiles from atomic models, Shape reconstruction,
Atomistic modeling


2:30 PM

Tutorial 3: Three-dimensional modeling from SAS data


3:15 PM

Coffee Break


3:30 PM

Guest Research Lecture - Thomas Grant, Research Asst. Professor, University
of Buffalo/Hauptman-Woodward Medical Research Institute


4:30 PM

SANS and Contrast Variation 


5:00 PM

Publishing SAS data 


5:30 PM

Conclusion

 
Pre-registration is mandatory. The fee to attend is: 

*   Student (undergrad, grad or postdoctoral) - $185 (CAN)
*   Corporate -  $355 (CAN)
*   Non-corporate or non-student - $185 (CAN)

Lunch will be included.
 
Contact: 
Kushol Gupta, Perelman School of Medicine, University of Pennsylvania.
 kgu...@upenn.edu
 
Confirmed Instructors:
 
Angela Criswell, Rigaku Corporation
Srinivas Chakravarthy, BioCAT Group, Advanced Photon Source
Richard Gillilan, Macromolecular Diffraction Facility, Cornell High Energy
Synchrotron Source
Thomas Grant, University of Buffalo/Hauptman-Woodward Medical Research
Institute
Jesse Hopkins, BioCAT Group, Advanced Photon Source
Maxim Petoukhov, BIOSAXS Group, EMBL Hamburg
 
More information is available at:
 
 http://www.amercrystalassn.org/2018-workshops   
 

http://www.amercrystalassn.org/2018-meeting-homepage 

 

 




 

[ccp4bb] Might be of interest to this group

[David Schuller]

http://www.cell.com/current-biology/fulltext/S0960-9822(18)30014-9


 A Novel Form of Stereo Vision in the Praying Mantis

Vivek Nityananda,Ghaith Tarawneh, Sid 
Henriksen,Diana Umeton,Adam Simmons, Jenny C.A. Read


DOI: https://doi.org/10.1016/j.cub.2018.01.012

Current Biology

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

[ccp4bb] ccp4 7.0 update 51

[Charles Ballard]

Dear All

just released is ccp4 7.0.051 containing

* phaser 2.8.2 

* dials 1.8.4

* ample 1.4.1

* simbad 0.10.1 (linux and osx)

* arcimboldo

Thanks to the authors of the software, and enjoy

CCP4 Core team

[ccp4bb] Marsden Funded PhD Project Available (New Zealand)

[Jodie Johnston]

Hi,


I am looking for a suitable student for a PhD project we have on offer and 
thought this might be the perfect place to find a suitably experienced 
candidate.

The project (Understanding protein communication networks) will involve a range 
of techniques (structural biology/protein chemistry/molecular biology) so a 
candidate with interest in proteins and some experience in these areas would be 
ideal.

The project is funded by funded by the Royal Society Te Apārangi Marsden Fund 
and full details of the project can be found at this link:

https://www.findaphd.com/search/ProjectDetails.aspx?PJID=95088

The project would be based in New Zealand; primarily at the Biomolecular 
Interaction Centre (http://www.canterbury.ac.nz/bic/) at the University of 
Canterbury, with some work carried out at the University of Auckland.

So if you would like to know more, or know of anyone who is interested/suitable 
and eager to come to NZ we are keen to hear from you.


Thanks.

Jodie


--
Dr Jodie Johnston
Senior Lecturer
Department of Chemical and Physical Sciences
University of Canterbury
Christchurch
New Zealand
e-mail: jodie.johns...@canterbury.ac.nz


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