[ccp4bb] PhD studentship on cryoEM data analysis

[Tom Burnley]

Posted on behalf of Peijun and Kevin:

Dear All,

A joint PhD studentship between Diamond Light Source and University of York
is available to Develop tools to automatically assess the quality and
resolution of cryoEM reconstructions. Please see the link below for
detailed information and how to apply.

http://www.diamond.ac.uk/Careers/Studentships/untitled0.html

Informal enquiries may be addressed to either supervisor:

Peijun Zhang, peijun.zh...@diamond.ac.uk, Diamond Light Source
Kevin Cowtan, kevin.cow...@york.ac.uk, University of York

-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em | www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] Research Technician for the Membrane Protein Laboratory (MPL) at Diamond Light Source and RCAH in Oxfordshire

[Dr. Isabel De Moraes]

Dear all,



Applications are invited for a full-time Research Technician position at the 
Membrane Protein Laboratory (MPL) located at the Diamond Light Source and at 
the Research Complex (Oxfordshire).

The MPL is Wellcome Trust funded facility created to allow scientists to 
determine medically relevant membrane protein structures more efficiently by 
combining recently developed high throughput technologies for protein 
production, crystallization, XFEL and EM. The MPL is located in laboratories 
around the ring at Diamond and also at the Research Complex at Harwell and 
equipped with state-of-the-art equipment.

The successful applicant will report directly to Dr Isabel Moraes, the MPL 
Group Leader. In the group he/she would assist in all aspects of the lab work, 
in particular repair and maintenance of crystallisation robots, assisting with 
training users in crystallisation with robots; production and crystallisation 
of membrane proteins. The technician will also be responsible for the general 
running of the laboratory, including placing orders, maintaining stocks of 
chemicals, preparing solutions, maintaining all the equipment and general 
laboratory maintenance. The applicant will also have a role in maintaining 
safety standards and documentation and have excellent communication skills.

For further details  about the position and how to apply please visit   
http://www.diamond.ac.uk/Careers/Vacancies/All/028_17_CH.html


Informal enquiries may be made to Dr Isabel Moraes, the MPL group leader 
(isabel.de-mor...@diamond.ac.uk)


Best regards,
Isabel Moraes

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[ccp4bb] Research Assistant for the Membrane Protein Laboratory (MPL) at Diamond Light Source and RCAH in Oxfordshire

[Dr. Isabel De Moraes]

Dear all,


Applications are invited for a full-time Research Assistant position at the 
Membrane Protein Laboratory (MPL) located at the Diamond Light Source and at 
the Research Complex (Oxfordshire).

The MPL is Wellcome Trust funded facility created to allow scientists to 
determine medically relevant membrane protein structures more efficiently by 
combining recently developed high throughput technologies for protein 
production, crystallization, XFEL and EM. The MPL is located in laboratories 
around the ring at Diamond and also at the Research Complex at Harwell and 
equipped with state-of-the-art equipment.

The successful applicant will report directly to Dr Isabel Moraes, the MPL 
Group Leader. In the group he/she will primarily assist the MPL users with 
molecular biology (cloning), expression in insect cell and mammalian, protein 
purification and/or crystallisation. In addition, the post holder should be 
familiar with all the facility equipment and also be involved in the in the 
day-to-day running of the laboratory, including equipment maintenance, ordering 
and health and safety procedures (Risk Assessments, GM forms and COOSH). The 
person will also be involved in sample preparation for EM and XFEL applications.

The successful candidate should have a Masters degree in biological sciences, 
or the equivalent in professional qualifications. In addition to good English 
verbal and written communication skills, methodical approaches to work and the 
ability to pay close attention to details is also desired.  You will also have 
good interpersonal and organisational skills as well as the ability to work as 
part of a team.

For further details  about the position and how to apply please visit   
http://www.diamond.ac.uk/Careers/Vacancies/All/027_17_CH.html


Informal enquiries may be made to Dr Isabel Moraes, the MPL group leader 
(isabel.de-mor...@diamond.ac.uk)


Best regards,
Isabel Moraes



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This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

[Andreas Förster]

Dear Pravin,

this brings me to re-emphasize a point I've just made at RapiData.  If
you're working with PILATUS or EIGER detectors, there is no good reason not
to spread your dose over at least 360° of data.  You will get better
statistics than if you collect 57.2° or whatever your strategy software
recommends - and you can laugh P1 in the face if it comes your way.  Just
make sure to adjust expose time or attenuation accordingly when expanding
your data collection to 360°.

This is of no help after data collection, but since you collected data for
SeMet SAD, you probably already have 360° or more and can thus work in P1
(as James suggested) without much pain.

All best.


Andreas



On Thu, Apr 20, 2017 at 12:11 AM, James Holton 
wrote:

>
> In situations like this I always try dropping to P1.  Even if the data are
> highly incomplete in P1 you can still refine it.  Difference maps are
> degraded by poor completeness, but you still might see something.  But
> either way, the R-factors will tell you something.  if dropping to P1
> solves your R-factor problems then you know you were in the wrong space
> group.
>
> The biggest caveat to dropping symmetry operators (and essentially
> replacing them with NCS operators) is that you want to be VERY careful not
> to mix your working and free sets.  The best way to do this is pick your
> free set with the highest-possible symmetry given your lattice, and then
> expand that to P1 using the CCP4 program "CAD".  Then you change the space
> group in "CAD" and it will chunk out the right asymmetric unit.  Oh, and
> then use PDBSET to expand your model to P1 as well.
> All this is done automatically by the program Zanuda, but even Zanuda
> cannot un-merge data.  You need to provide the P1 structure factors and
> then see what it tells you.
>
> Does that help?
>
> -James Holton
> MAD Scientist
>
> On 4/18/2017 5:56 PM, gnufreebsd wrote:
>
> Dear Pravin
> for a kinase, n lobe is quite flexible ,  especially beta1 and beta2, and
> residues beyond theses two strands.
>
>
> best regards
> tiger
>
> 发自 WPS邮箱客戶端 
> 在 Pravinkumar Jagtap  
> ，2017年4月12日 上午2:55写道：
>
> Dear All,
> I am stuck with this problem for 2 months and hope you could help.
>
> We have a 2.1 A dataset for a 380 amino acid long protein. The space group
> is I4 (single molecule in asymmetric unit, 48% solvent content) and the
> dataset is quite perfect (no obvious pathologies). The protein itself is
> organised in 2 lobes (N and C terminal lobes). The sequence identity to
> nearest homologue structure is 17%.
>
> We could  get the phases by SeMet SAD phasing (3A resolution dataset, 5
> SeMet (excluding N-terminal Met), 3 full occupancy SeMet in C-terminal lobe
> and 2 partial occupancy (~0.5 each; present on surface) SeMet in N-terminal
> lobe). Automated  model building (at 2.1 A) yielded nice model for the
> C-terminal lobe (215 residues)  and manually I could build parts (around 80
> residues) of N-terminal lobe with high confidence. In addition we could
> also build a ligand which is sandwiched between C and N terminal lobe.
>
> However the Rfree is stuck at 0.39 (Rwork 0.33). There is indeed some
> patchy density left at the N terminal lobe but as it is discontinuous, I
> cannot build anything in it (except lots of water molecules). In total I am
> missing around 85 residues. These residues are predicted to be present in
> secondary structure (and not flexible).
>
> As I have around 75-80% model built, I would expect that I would have all
> the phases and  should get nice density for the remaining part. But as I
> dont see it, could the rest part be flexible? But again, this is not
> reflected in the R factors (I would then expect low Rfree).
>
> Could it be that I still lack phases (due to partial occupancy of SeMeth
> in N-terminal lobe ) and have to try to get them by heavy metal soaking, or
> there is disorder in the N-terminal lobe? I have also tried solving
> different datasets for same crystal but this has not been useful.
>
> Regards,
> Pravin.
>
>
>


-- 

Andreas Förster, Ph.D.
MX Application Scientist, Scientific Sales
Phone: +41 56 500 2100 <+41%2056%20500%2021%2000> | Direct: +41 56 500 21 76
<+41%2056%20500%2021%2076> | Email: andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com

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