[ccp4bb] Postdoctoral fellowship in structure-guided drug discovery

[Marko Hyvonen]

Postdoctoral fellowship available in a collaborative structure-guided drug 
discovery project between my group and groups of Sharon Rossiter and Stewart 
Kirton at University of Hertfordshire, funded by the Hertfordshire Science 
Partnership Therapy Accelerator scheme.


Successful candidate will be part of a multidisciplinary team exploring novel 
inhibitors of a cancer drug target  protein. The position offers access to the 
state of the art laboratory facilities at the University of Cambridge and the 
University of Hertfordshire, plus the opportunity to work at the dynamic 
industry/academia interface of the  Stevenage BioScience Catalyst campus 
(http://www.stevenagecatalyst.com/). The postdoctoral fellow will develop and 
optimise biophysical methods for high-throughput screening of inhibitors, 
measurement of inhibitor-protein interactions, crystallographic elucidation of 
ligand-protein complexes and fragment-based approaches to discovering novel 
inhibitor scaffolds as a potential therapy for pancreatic cancer.


Applicants should possess (or about to obtain) a doctorate in biochemistry, 
chemistry, structural biology or a closely related subject. Experience in 
molecular cloning, protein expression, purification and characterisation, 
biophysical analysis of protein-ligand interactions and protein crystallography 
are essential for this post, previous experience in structure-guided drug 
discovery a definite advantage.


More details of the positions and on how to apply can be found through the link 
below and on the website of University of Hertfordshire (https://www.jobs.herts.ac.uk).


Informal enquiries can  be sent to Dr Sharon Rossiter (s.rossi...@herts.ac.uk) 
or myself.


http://www.jobs.ac.uk/job/BGL627/postdoctoral-research-fellow-in-structure-guided-drug-discovery/

Marko

--

Marko Hyvonen
Department of Biochemistry, University of Cambridge
mh...@cam.ac.uk
+44 (0)1223 766 044
@HyvonenGroup
http://hyvonen.bioc.cam.ac.uk

Re: [ccp4bb] coordinate transformation

[James Holton]

What I usually do for this is make a copy of the PDB file and change all 
the atom x-y-z positions to "1.000".  Then I use something like 
reforigin or my "origins.com" script to shift the original coordinates 
via allowed symmetry operations, origin shifts, or perhaps indexing 
ambiguities until it is as close as possible to the "reference", which 
is at 1,1,1.  I use 1,1,1 instead of 0,0,0 because there are generally 
at least two symmetry-equivalent places that are equidistant from the 
origin. Declaring the reference to be a bit off-center breaks that 
ambiguity, and also biases the result toward having all-positive x,y,z 
values.



In case it is interesting, my script is here:

http://bl831.als.lbl.gov/~jamesh/scripts/origins.com


You need to have the CCP4 suite set up for it to work.  Run it with no 
arguments to get instructions.



-James Holton

MAD Scientist


On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:


Hello,

If someone could point this out would be very helpful... Wasnt there a 
simple script somewhere that would transfer coordinates close to 
origin - if they for some reason are not? Just cant find anything 
right away. Sure i have done this before...



Thanks,

Tommi

[ccp4bb] Post-Master’s Research Associate

[O'Neill, Hugh Michael]

Opportunity
Post-Master’s Research Associate
Organization
Oak Ridge National Laboratory (ORNL)
Reference Code
ORNL18-07-NSD
https://www.zintellect.com/Posting/Details/3817
Academic Levels
·   Post-Master's
Description

The Neutron Sciences Directorate (NScD) at Oak Ridge National Laboratory 
operates the High Flux Isotope Reactor (HFIR), the United States' highest flux 
reactor based neutron source, and the Spallation Neutron Source (SNS), the 
world's most intense pulsed accelerator based neutron source. Together these 
facilities operate 24 instruments for neutron scattering research, each year 
carrying out 1000 experiments in the physical, chemical, materials, biological 
and medical sciences for 2000 visiting scientists. HFIR also provides unique 
facilities for isotope production and neutron irradiation. To learn more about 
Neutron Sciences at ORNL go to: http://neutrons.ornl.gov.

The Neutron Scattering Division (NSD) invites applications for a M.S. 
biochemist/molecular biologist to join the Large Scale Structures Group at Oak 
Ridge National Laboratory (ORNL).

Major Duties/Responsibilities:

*Responsible for protein production, protein labeling, purification, 
development of novel labeling strategies

*Assist in protein crystallography, small-angle scattering studies

*Assist in preparation of scientific papers

*Ensure compliance with environment, safety, health and quality program 
requirements

*Maintain strong commitment to the implementation and perpetuation of values 
and ethics
Qualifications

A M.S. degree in the biological sciences (biochemistry, molecular biology, 
biotechnology) is required. The successful candidate will have understanding 
and experience of molecular biology and preparative biochemical techniques, 
including expression and purification of recombinant proteins from bacterial 
and eukaryotic sources.  Expertise with recombinant DNA techniques including 
PCR, DNA cloning, mutagenesis, and protein expression is required. Additional 
expertise in membrane protein expression/purification would be a distinct 
advantage. The candidate should be self-motivated, have good interpersonal 
communication and presentational skills as well as a demonstrated ability to 
work effectively with staff at all levels within a multi-disciplinary team.

The ORNL Postgraduate Research Associates Program is administered by Oak Ridge 
Associated Universities through its contract with the U.S. Department of Energy 
to manage the Oak Ridge Institute for Science and Education (ORISE).

Eligibility Requirements
·   Degree: Currently pursuing a Master's degree or have received this 
degree within 60 months.

ORAU is an Equal Opportunity Employer (EOE AA M/F/Vet/Disability); visit the 
ORAU website for required employment 
notices.

Re: [ccp4bb] coordinate transformation

[Eleanor Dodson]

I use PISA for the compact molecule construction - it works very well, and
probably should be the default at the end of every MR - it also tries to
choose a sensible symm op which allows assemblies to be generated easily.

But then you would have to think about how to position that assembly as
close to the origin as possible.

One way to buld on my script would be to search distances between the
centre of mass and all alternate origins - easy fenough or non-polar SGs ..
Eleanor

On 14 December 2017 at 16:38, Edward A. Berry  wrote:

> On 12/14/2017 04:34 AM, Tim Gruene wrote:
>
>> Dear Tommi,
>>
>> 1.
>
>> if you only need to consider translations, and not other symmetry
>> operations,
>> you can use moleman2, convert coordinates to fractional ones and add or
>> substract the integer that brings the centre of mass closest to 0.
>>
>> 2.
>
>> In case you want to take the symmetry operations into account, you would
>> have
>> to check for each operator, which one brings the centre of mass closest
>> to 0.
>> This could most likely be scripted with moleman2.
>>
>> 3. If you also want to consider origin shifts (in spacegroups where
> alternate origins exist) the achesym site does that. (If you can't bring
> the molecule to the origin, bring the origin to the molecule)
>
> 4. If you also want to pack multiple chains that may have been built in
> various locations into a compact multimer, the achesym site does that.
>
> But no, it's not a simple script.
> And I believe the achesym site works not so much to put the center of mass
> near the origin, but to put as many atoms as possible in first unit cell
> (0 is then a secondary priority.
>
>
> Best,
>> Tim
>>
>> On Thursday, December 14, 2017 8:39:48 AM CET Kajander, Tommi A wrote:
>>
>>> Dear Paul,
>>>
>>>
>>> Yes thank you. This was the best answer i think. Someone else already
>>> also
>>> suggested that also.  Coot is very handy indeed.
>>>
>>>
>>> (Would still be curious of knowing how to find the "closest to origin"
>>> copy
>>> otherwise - but this solves my problem)
>>>
>>>
>>> Thanks to all who responded.
>>>
>>>
>>> Cheers,
>>>
>>> Tommi
>>>
>>> 
>>> From: CCP4 bulletin board  on behalf of Paul
>>> Emsley
>>>  Sent: Thursday, December 14, 2017 3:25:19 AM
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: Re: [ccp4bb] coordinate transformation
>>>
>>> On 13/12/2017 13:50, Kajander, Tommi A wrote:
>>>
 Hello,

 If someone could point this out would be very helpful... Wasnt there a
 simple script somewhere that would transfer coordinates close to origin
 -
 if they for some reason are not? Just cant find anything right away.

>>> At the risk of not answering the question because it's not a simple
>>> script,
>>> my I recommend Coot?
>>>
>>> File -> Open -> yourcoords.cif
>>> Draw -> Cell & Symm -> Master Switch -> Yes
>>> Show Unit Cells -> Yes
>>> OK
>>> Drag the View to the Origin # it's marked with an "O"
>>> Middle-mouse click on an Symmetry-related Atom # that's close to the
>>> origin
>>> Extensions -> Modelling -> Symm Shift Reference Chain Here
>>>
>>
>> --
>> --
>> Paul Scherrer Institut
>> Tim Gruene
>> - persoenlich -
>> OFLC/104
>> CH-5232 Villigen PSI
>> phone: +41 (0)56 310 5297
>>
>> GPG Key ID = A46BEE1A
>>
>>

[ccp4bb] Post Doctoral Structural Biology Position Icahn School of Medicine at Mount Sinai NY

[Brian Krumm]

Posted on behalf of a colleague, please respond directly to the e-mail address 
below.


Postdoctoral Position in Structure and Function of G protein-coupled Serotonin 
Receptors and Neurotransmitter Transporters.
 
A postdoctoral position is available in the research group of Daniel Wacker, 
Department of Pharmacological Sciences, Icahn School of Medicine at Mount 
Sinai, New York. Employment will commence in early Spring of 2018.
 
The long term goal of the Wacker lab is to understand the structure, function 
and pharmacology of G protein-coupled serotonin receptors and neurotransmitter 
transporters, and leverage these data using structure based drug design to 
develop novel therapeutics. Serotonin signaling in the brain controls a variety 
of physiology related to mental health, including cognition, learning, and 
memory, and is targeted by illicit and therapeutic psychoactive drugs such as 
LSD, antidepressants, and anti-psychotics. Towards a molecular understanding of 
serotonin signaling, we will employ a combination of state-of-the-art 
structural (X-ray crystallography, cryo-EM) and pharmacological techniques.
 
More information can be found at http://wackerlab.com/.
 
Applicants should hold a PhD in a relevant subject area, such as membrane 
protein biochemistry or structural biology. Experience in recombinant membrane 
protein expression and purification, structure determination, or functional 
analysis using biochemical and biophysical techniques is essential. The ability 
to work in a team as well as good verbal and written communication skills are 
expected. Experience in protein x-ray crystallography and/or cryo-EM is an 
advantage.
 
Applications including research interests and career aims, as well as a CV with 
publication record and contact information for three references should be send 
to:
 
Daniel Wacker, PhD
Assistant Professor
Department of Pharmacological Sciences
Icahn School of Medicine at Mount Sinai
One Gustave L. Levy Place
New York, NY 10029

daniel.wac...@mssm.edu

Re: [ccp4bb] Crystal structure of an unknown protein

[Edward A. Berry]

In this case you know the protein is closely relaed to whatefer contaminer 
found, and you have good sequence data, so I agree the next step is blast. 
Maybe it is an isozyme of the structure used.

In cases where you solve an unknown by heavy atom derivatives and have no idea 
what it is; and the resolution is too low to get a good read on the sequence, 
but you can trace the chain; the DALI server is the way to go. That is how we 
identified 4HEI.

On 12/14/2017 07:08 AM, Jiyong Su wrote:

Dear CCP4bb,

In 2014, I collected a high quality data set from a crystal. But I could not 
solve the structure of that crystal because this protein is a contaminate.
Recently, I used StruBE's Contaminer and fortunately got the solution. Thanks 
ContaMiner!!!  This protein is a contaminate protein.

However, I found this protein is an unknown protein (about 180 residues) whose 
amino acid sequence is not totally same as E.coli. There are about 20 point 
mutation sites comparing to the E.coli protein. This means this protein may be 
from an unknown bacteria.

The space group of this crystal is new. There is also a new ligand in this 
protein.

My question is how could I found the primary structure of this protein and how 
to deposit this protein in PDB.

Best regards,

Jiyong

Re: [ccp4bb] coordinate transformation

[Edward A. Berry]

On 12/14/2017 04:34 AM, Tim Gruene wrote:

Dear Tommi,


1.

if you only need to consider translations, and not other symmetry operations,
you can use moleman2, convert coordinates to fractional ones and add or
substract the integer that brings the centre of mass closest to 0.


2.

In case you want to take the symmetry operations into account, you would have
to check for each operator, which one brings the centre of mass closest to 0.
This could most likely be scripted with moleman2.


3. If you also want to consider origin shifts (in spacegroups where alternate 
origins exist) the achesym site does that. (If you can't bring the molecule to 
the origin, bring the origin to the molecule)

4. If you also want to pack multiple chains that may have been built in various 
locations into a compact multimer, the achesym site does that.

But no, it's not a simple script.
And I believe the achesym site works not so much to put the center of mass near the 
origin, but to put as many atoms as possible in first unit cell (0 on behalf of Paul Emsley
 Sent: Thursday, December 14, 2017 3:25:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coordinate transformation

On 13/12/2017 13:50, Kajander, Tommi A wrote:

Hello,

If someone could point this out would be very helpful... Wasnt there a
simple script somewhere that would transfer coordinates close to origin -
if they for some reason are not? Just cant find anything right away.

At the risk of not answering the question because it's not a simple script,
my I recommend Coot?

File -> Open -> yourcoords.cif
Draw -> Cell & Symm -> Master Switch -> Yes
Show Unit Cells -> Yes
OK
Drag the View to the Origin # it's marked with an "O"
Middle-mouse click on an Symmetry-related Atom # that's close to the origin
Extensions -> Modelling -> Symm Shift Reference Chain Here


--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/104
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

[ccp4bb] ccp4online webservices

[Charles Ballard]

Dear All

just a heads up that these will be unavailable from 3pm GMT on Friday 15th 
until the following Monday as we go through fixed line testing on the electrics.

Sorry for any inconvenience

Charles

Re: [ccp4bb] coordinate transformation

[Eleanor Dodson]

Here is  a VERY oldfashioned solution.

Find the centre of mass of your molecule.

pdbset xyzin mol.pdb
end
tells you that

Make a mini PDB with the CRYST1 record, and two "atoms" - one at 0 0 0, the
other at the centre of mass with some atom type say C

then distang xyzin min.pdb
radi C  20 say
dist all
end

This will give you the symmetry equalent for the Centre f Mass transformed
by all symmetry operators

Then apply that symmetry operator to your coordinates..

BUT this will NOT have checked the best origin shift..

That is another problem..
Eleanor


And Yes Randy - I am sure this could be done more easily and elegantly in
Python..

On 14 December 2017 at 09:34, Tim Gruene  wrote:

> Dear Tommi,
>
> if you only need to consider translations, and not other symmetry
> operations,
> you can use moleman2, convert coordinates to fractional ones and add or
> substract the integer that brings the centre of mass closest to 0.
>
> In case you want to take the symmetry operations into account, you would
> have
> to check for each operator, which one brings the centre of mass closest to
> 0.
> This could most likely be scripted with moleman2.
>
> Best,
> Tim
>
> On Thursday, December 14, 2017 8:39:48 AM CET Kajander, Tommi A wrote:
> > Dear Paul,
> >
> >
> > Yes thank you. This was the best answer i think. Someone else already
> also
> > suggested that also.  Coot is very handy indeed.
> >
> >
> > (Would still be curious of knowing how to find the "closest to origin"
> copy
> > otherwise - but this solves my problem)
> >
> >
> > Thanks to all who responded.
> >
> >
> > Cheers,
> >
> > Tommi
> >
> > 
> > From: CCP4 bulletin board  on behalf of Paul
> Emsley
> >  Sent: Thursday, December 14, 2017 3:25:19 AM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] coordinate transformation
> >
> > On 13/12/2017 13:50, Kajander, Tommi A wrote:
> > > Hello,
> > >
> > > If someone could point this out would be very helpful... Wasnt there a
> > > simple script somewhere that would transfer coordinates close to
> origin -
> > > if they for some reason are not? Just cant find anything right away.
> > At the risk of not answering the question because it's not a simple
> script,
> > my I recommend Coot?
> >
> > File -> Open -> yourcoords.cif
> > Draw -> Cell & Symm -> Master Switch -> Yes
> > Show Unit Cells -> Yes
> > OK
> > Drag the View to the Origin # it's marked with an "O"
> > Middle-mouse click on an Symmetry-related Atom # that's close to the
> origin
> > Extensions -> Modelling -> Symm Shift Reference Chain Here
>
> --
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OFLC/104
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
>

Re: [ccp4bb] Crystal structure of an unknown protein

[Keller, Jacob]

Wow, pretty cool—you must have solved it to very high resolution to know the 
sequence from the structure. I cannot imagine, however, how you got this 
contaminant—maybe phage infection of your bacterial culture? Anyway, I agree 
with BLAST-ing the sequence, seeing what you get that is closest.

JPK


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jiyong Su
Sent: Thursday, December 14, 2017 7:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Crystal structure of an unknown protein

Dear CCP4bb,

In 2014, I collected a high quality data set from a crystal. But I could not 
solve the structure of that crystal because this protein is a contaminate.
Recently, I used StruBE's Contaminer and fortunately got the solution. Thanks 
ContaMiner!!!  This protein is a contaminate protein.

However, I found this protein is an unknown protein (about 180 residues) whose 
amino acid sequence is not totally same as E.coli. There are about 20 point 
mutation sites comparing to the E.coli protein. This means this protein may be 
from an unknown bacteria.

The space group of this crystal is new. There is also a new ligand in this 
protein.

My question is how could I found the primary structure of this protein and how 
to deposit this protein in PDB.

Best regards,

Jiyong

Re: [ccp4bb] Crystal structure of an unknown protein

[Pedro Matias]

Hello,

Welcome to the club of unexpected results!

You don't provide a lot of background, but based on what you wrote you can:

1. Do a BLAST search using a known part of your sequence to find whether
this sequence has been deposited.

2. Assign the different residues based on the chemical environment and
electron density and refine the structure.

I'm sure you can submit the refined structure to the PDB even from an
unknown protein.

Regards,

Pedro Matias


Às 12:08 de 14/12/2017, Jiyong Su escreveu:
> Dear CCP4bb,
>
> In 2014, I collected a high quality data set from a crystal. But I
> could not solve the structure of that crystal because this protein is
> a contaminate. 
> Recently, I used StruBE's Contaminer and fortunately got the solution.
> Thanks ContaMiner!!!  This protein is a contaminate protein. 
>
> However, I found this protein is an unknown protein (about 180
> residues) whose amino acid sequence is not totally same as E.coli.
> There are about 20 point mutation sites comparing to the E.coli
> protein. This means this protein may be from an unknown bacteria.  
>
> The space group of this crystal is new. There is also a new ligand in
> this protein. 
>
> My question is how could I found the primary structure of this protein
> and how to deposit this protein in PDB. 
>
> Best regards,
>
> Jiyong
>

-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8

[ccp4bb] Crystal structure of an unknown protein

[Jiyong Su]

Dear CCP4bb,


In 2014, I collected a high quality data set from a crystal. But I could not 
solve the structure of that crystal because this protein is a contaminate. 
Recently, I used StruBE's Contaminer and fortunately got the solution. Thanks 
ContaMiner!!!  This protein is a contaminate protein. 


However, I found this protein is an unknown protein (about 180 residues) whose 
amino acid sequence is not totally same as E.coli. There are about 20 point 
mutation sites comparing to the E.coli protein. This means this protein may be 
from an unknown bacteria.  


The space group of this crystal is new. There is also a new ligand in this 
protein. 


My question is how could I found the primary structure of this protein and how 
to deposit this protein in PDB. 


Best regards,


Jiyong

Re: [ccp4bb] coordinate transformation

[Tim Gruene]

Dear Tommi,

if you only need to consider translations, and not other symmetry operations, 
you can use moleman2, convert coordinates to fractional ones and add or 
substract the integer that brings the centre of mass closest to 0.

In case you want to take the symmetry operations into account, you would have 
to check for each operator, which one brings the centre of mass closest to 0. 
This could most likely be scripted with moleman2.

Best,
Tim

On Thursday, December 14, 2017 8:39:48 AM CET Kajander, Tommi A wrote:
> Dear Paul,
> 
> 
> Yes thank you. This was the best answer i think. Someone else already also
> suggested that also.  Coot is very handy indeed.
> 
> 
> (Would still be curious of knowing how to find the "closest to origin" copy
> otherwise - but this solves my problem)
> 
> 
> Thanks to all who responded.
> 
> 
> Cheers,
> 
> Tommi
> 
> 
> From: CCP4 bulletin board  on behalf of Paul Emsley
>  Sent: Thursday, December 14, 2017 3:25:19 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] coordinate transformation
> 
> On 13/12/2017 13:50, Kajander, Tommi A wrote:
> > Hello,
> > 
> > If someone could point this out would be very helpful... Wasnt there a
> > simple script somewhere that would transfer coordinates close to origin -
> > if they for some reason are not? Just cant find anything right away.
> At the risk of not answering the question because it's not a simple script,
> my I recommend Coot?
> 
> File -> Open -> yourcoords.cif
> Draw -> Cell & Symm -> Master Switch -> Yes
> Show Unit Cells -> Yes
> OK
> Drag the View to the Origin # it's marked with an "O"
> Middle-mouse click on an Symmetry-related Atom # that's close to the origin
> Extensions -> Modelling -> Symm Shift Reference Chain Here

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/104
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


signature.asc
Description: This is a digitally signed message part.

Re: [ccp4bb] coordinate transformation

[Kajander, Tommi A]

Dear Paul,


Yes thank you. This was the best answer i think. Someone else already also 
suggested that also.  Coot is very handy indeed.


(Would still be curious of knowing how to find the "closest to origin" copy 
otherwise - but this solves my problem)


Thanks to all who responded.


Cheers,

Tommi


From: CCP4 bulletin board  on behalf of Paul Emsley 

Sent: Thursday, December 14, 2017 3:25:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coordinate transformation

On 13/12/2017 13:50, Kajander, Tommi A wrote:
> Hello,
>
> If someone could point this out would be very helpful... Wasnt there a simple 
> script somewhere that would
> transfer coordinates close to origin - if they for some reason are not? Just 
> cant find anything right away.
>

At the risk of not answering the question because it's not a simple script, my 
I recommend Coot?

File -> Open -> yourcoords.cif
Draw -> Cell & Symm -> Master Switch -> Yes
Show Unit Cells -> Yes
OK
Drag the View to the Origin # it's marked with an "O"
Middle-mouse click on an Symmetry-related Atom # that's close to the origin
Extensions -> Modelling -> Symm Shift Reference Chain Here

[ccp4bb] Scientific programmer vacancy to work with EM validation

[Ardan Patwardhan]

Dear all

We are part of a consortium which has recently been funded by the Wellcome 
Trust to develop and disseminate validation tools to assess the quality of 
cryoEM reconstructions and fitted models. The other members of the project are 
STFC, Francis Crick Institute, Birkbeck College, University of Manchester, and 
the MRC Laboratory of Molecular Biology.

We are looking for a scientific programmer tol:
• Expand and improve the repertoire of stand-alone validation servers 
for the EM community offered by EMBL-EBI, such as the Fourier Shell Correlation 
server (emdb-empiar.org/fsc) and the Tilt Pair Validation server 
(emdb-empiar.org/tiltpair)
• Expand the visual analysis web service (e.g., 
emdb-empiar.org/emd-984/analysis) that provides validation information on EMDB 
entries with the components to be developed by project partners
• Develop reporting formats for depositing validation information, 
e.g., from local resolution methods such as ResMap.

Qualifications and Experience

Applicants should have a Masters/PhD degree in a structural biology related 
field (e.g., 3DEM, X-ray crystallography, and NMR) and at least one years 
experience in software development (preferably related to a structural biology 
project). Applicants should have a good understanding of the image formation 
and image processing concepts in at least one structural field and be prepared 
to learn relevant concepts for the project. 

Excellent written and oral communication skills, fluency in English, ability to 
work in a team, and attention to detail are required. The position may require 
occasional travel, mainly in the UK.

More details can be found here:  
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01094=1 

Please feel free to email me (ar...@ebi.ac.uk ) for 
informal enquiries.
The closing date for the application is 2nd January 2018

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