[ccp4bb] Deadline for rapid access proposals at eBIC@Diamond

[Martin Walsh]

Dear all – we are extending the 1st January 2017 deadline for rapid access 
proposals at eBIC to the 8th January 2017 
(http://www.diamond.ac.uk/Science/Integrated-facilities/eBIC/How-to-apply.html)

Happy christmas

Martin

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Re: [ccp4bb] Crystal with ZERO diffraction

[James Phillips]

I call these crystals as examples of Space Groups 231 where all reflections
are systematically absent.

Happy Solstice to everyone. The will be more daylight tomorrow (Northern
Hemisphere).


On Wed, Dec 21, 2016 at 1:44 PM, Tom Huxford  wrote:

> Dear ccp4b collective mind and experience,
>
> Greetings from San Diego.
>
> I have done my fair share of synchrotron data collection on many diverse
> macromolecular crystal systems.  But this weekend was the first time that I
> ever shot crystals that failed to diffract entirely.
>
> Details:  we have purified and crystallized an ~90 kDa proteolytic
> fragment containing a single point mutant version of a myosin motor domain
> in complex with a separate light chain polypeptide.  The crystals are
> relatively small (10-30 microns in each dimension) but clearly crystalline
> in character (clear faces, edges, and facets).  The crystals tested
> positive for protein by absorbance at 280 nm.  This weekend we tested more
> than 40 of them for diffraction in different cryo solvents and did not
> observe a single identifiable diffracted ray.  It was as if we had only
> cryo on the end of our loops.  Increasing the time of exposure or annealing
> did nothing to improve the situation.  Crystals from a different protein
> system that we also tested this weekend on the same beamline diffracted to
> beyond 1.3 Å.
>
> I only post this because, in my experience, crystals of this size and
> superficial quality always give some signal--even if it is horrifyingly
> bad.  But never complete diffraction silence.  We will work this week to
> identify what it is that we "crystallized".  But can anybody who has had a
> similar experience suggest what it is that could be going on here?
>
> Thanks in advance for any responses.  And happy holidays to us all.
>
> Tom Huxford.
> ==
> Tom Huxford.
> Structural Biochemistry Laboratory
> Department of Chemistry & Biochemistry
> San Diego State University
> (619) 594-1606
>
>

[ccp4bb] [Job] Postdoctoral Fellow Position in Structural Bioinformatics at UC San Diego

[Rose, Peter]

We are looking for a highly motivated postdoc as part of our new project 
“Compressive Structural Bioinformatics” funded by the US National Institutes of 
Health (NIH) Big Data to Knowledge (BD2K) initiative.

The Challenge: To enable efficient research on the rapidly growing number of 3D 
molecular structures of ever increasing size and complexity. Current algorithms 
used in Structural Bioinformatics do not scale well with the rapid growth in 
structural data. In this project, we will employ the latest advances in 
computer science to develop highly scalable, distributed parallel algorithms to 
overcome these limitations.

Qualifications: Ph.D. in one or more of the following research areas

·   Computer Science with a focus on large scale scientific computing

·   Structural Bioinformatics with a focus on new methods development

·   Computational Structural Biology with a focus on improved structure 
solution methods

Experience with the development and performance optimization of scientific 
software. Demonstrated proficiency in a high-level programming language, such 
as Java or Python and experience with state of the art software development 
tools. Strong skills in applied mathematics and algorithm design are required. 
Experience with JavaScript and web development is a plus. High productivity 
demonstrated by publications and contributions to open source software 
projects. Experience in the development and application of modern distributed 
parallel computing environments, such as Apache Big Data projects including 
Apache Spark is a plus. Excellent interpersonal, written, and oral presentation 
skills are essential.

Note, this position is reviewed annually on the basis of performance and can be 
renewed for a maximum of two years.

Our Environment:

The Structural Bioinformatics Lab at the San Diego Supercomputer Center (SDSC) 
(http://www.sdsc.edu) is involved in research and 
development activities centered around 3D structures of proteins and nucleic 
acids, the integration of structural data with other domains such as Medicine, 
Genomics, Biology, Drug Discovery, and the development of scalable solution to 
Big Data problems in Structural Bioinformatics. Our group collaborates closely 
with the RCSB Protein Data Bank (PDB) 
(http://www.rcsb.org) west-coast operations at UCSD. As 
part of the NIH BD2K initiative, we have developed a compact file format for 
ultrafast processing of 3D macromolecular structures (http://mmtf.rcsb.org).

As an Organized Research Unit of UC San Diego, SDSC is a world leader in 
data-intensive computing and cyber infrastructure, providing resources, 
services, and expertise to the national research community, including industry 
and academia.

To apply, please send cover letter and resume to Dr. Peter Rose 
(pwr...@ucsd.edu), no later than January 31, 2017.

--
Peter Rose, Ph.D.
Director, Structural Bioinformatics Laboratory
San Diego Supercomputer Center (http://www.sdsc.edu)
University of California, San Diego
+1-858-822-5497

Re: [ccp4bb] Crystal with ZERO diffraction

[Gloria Borgstahl]

I have learned to refrain from catapulting my crystals.

Happy holidays, God bless us ... everyone (with diffracting crystals)

On Wed, Dec 21, 2016 at 2:35 PM, Keller, Jacob 
wrote:

> >In a second case we were working on a beamline on the west coast of the
> US. Every crystal we put on vanished before we could even collect data –
> the loops appeared empty as soon as we looked through the microscope (this
> sets the decade). The beamline had an extra strong magnet on the goniometer
> and on closer inspection we saw that the hutch wall next to the goniometer
> was peppered with many crystals - they were being catapulted out of the
> loop when the base ‘flipped’ onto the magnet. There were so many that
> others will know this beamline.
>
>
>
> Yes, I also catapulted some crystals—but I actually saw one of mine fly
> off the loop….
>
>
>
> JPK
>
>
>

Re: [ccp4bb] Crystal with ZERO diffraction

[Thomas, Leonard M.]

Just my  2 cents worth, I am with others in that this is actually not unusual.  
Outside of what Patrick said the first thing to look at if you  can is does the 
crystal diffract at all.  You can do this by taking a room temperature shot, 
the Mitegen loop/sleeve/pins work well for a quick shot or if you have 
capillaries you can use them too. I have had cryo's kill more crystals then I 
can remember.

Cheers,
Len Thomas


From: CCP4 bulletin board  on behalf of Patrick Loll 

Sent: Wednesday, December 21, 2016 2:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Crystal with ZERO diffraction

Sadly, I have seen numerous examples of reasonably-sized crystals that give no 
observable ordered diffraction (I shot a few this weekend, in fact). I can’t 
give you evidence for what is happening, but I guess that you can build a 
macroscopic assembly using lattice interactions that are only modestly 
specific, resulting in a structure that is highly disordered internally, even 
though it looks OK visually (the jello model). Alternatively, you may have a 
crystal that was originally well-ordered but subsequently decayed; however, it 
failed to dissolve because proteins at the surface became cross-linked and held 
everything together (the soup dumpling model).

So no suggestions as how to proceed (except to follow Eddie’s sage advice to 
grow more/different crystals), but I can assure you that you’re not alone in 
observing this.

Cheers,

Pat Loll

> On 21 Dec 2016, at 2:44 PM, Tom Huxford  wrote:
>
> Dear ccp4b collective mind and experience,
>
> Greetings from San Diego.
>
> I have done my fair share of synchrotron data collection on many diverse 
> macromolecular crystal systems.  But this weekend was the first time that I 
> ever shot crystals that failed to diffract entirely.
>
> Details:  we have purified and crystallized an ~90 kDa proteolytic fragment 
> containing a single point mutant version of a myosin motor domain in complex 
> with a separate light chain polypeptide.  The crystals are relatively small 
> (10-30 microns in each dimension) but clearly crystalline in character (clear 
> faces, edges, and facets).  The crystals tested positive for protein by 
> absorbance at 280 nm.  This weekend we tested more than 40 of them for 
> diffraction in different cryo solvents and did not observe a single 
> identifiable diffracted ray.  It was as if we had only cryo on the end of our 
> loops.  Increasing the time of exposure or annealing did nothing to improve 
> the situation.  Crystals from a different protein system that we also tested 
> this weekend on the same beamline diffracted to beyond 1.3 Å.
>
> I only post this because, in my experience, crystals of this size and 
> superficial quality always give some signal--even if it is horrifyingly bad.  
> But never complete diffraction silence.  We will work this week to identify 
> what it is that we "crystallized".  But can anybody who has had a similar 
> experience suggest what it is that could be going on here?
>
> Thanks in advance for any responses.  And happy holidays to us all.
>
> Tom Huxford.
> ==
> Tom Huxford.
> Structural Biochemistry Laboratory
> Department of Chemistry & Biochemistry
> San Diego State University
> (619) 594-1606
>

Re: [ccp4bb] Crystal with ZERO diffraction

[Patrick Loll]

Sadly, I have seen numerous examples of reasonably-sized crystals that give no 
observable ordered diffraction (I shot a few this weekend, in fact). I can’t 
give you evidence for what is happening, but I guess that you can build a 
macroscopic assembly using lattice interactions that are only modestly 
specific, resulting in a structure that is highly disordered internally, even 
though it looks OK visually (the jello model). Alternatively, you may have a 
crystal that was originally well-ordered but subsequently decayed; however, it 
failed to dissolve because proteins at the surface became cross-linked and held 
everything together (the soup dumpling model).

So no suggestions as how to proceed (except to follow Eddie’s sage advice to 
grow more/different crystals), but I can assure you that you’re not alone in 
observing this.

Cheers,

Pat Loll
 
> On 21 Dec 2016, at 2:44 PM, Tom Huxford  wrote:
> 
> Dear ccp4b collective mind and experience,
> 
> Greetings from San Diego.
> 
> I have done my fair share of synchrotron data collection on many diverse 
> macromolecular crystal systems.  But this weekend was the first time that I 
> ever shot crystals that failed to diffract entirely.
> 
> Details:  we have purified and crystallized an ~90 kDa proteolytic fragment 
> containing a single point mutant version of a myosin motor domain in complex 
> with a separate light chain polypeptide.  The crystals are relatively small 
> (10-30 microns in each dimension) but clearly crystalline in character (clear 
> faces, edges, and facets).  The crystals tested positive for protein by 
> absorbance at 280 nm.  This weekend we tested more than 40 of them for 
> diffraction in different cryo solvents and did not observe a single 
> identifiable diffracted ray.  It was as if we had only cryo on the end of our 
> loops.  Increasing the time of exposure or annealing did nothing to improve 
> the situation.  Crystals from a different protein system that we also tested 
> this weekend on the same beamline diffracted to beyond 1.3 Å.
> 
> I only post this because, in my experience, crystals of this size and 
> superficial quality always give some signal--even if it is horrifyingly bad.  
> But never complete diffraction silence.  We will work this week to identify 
> what it is that we "crystallized".  But can anybody who has had a similar 
> experience suggest what it is that could be going on here?
> 
> Thanks in advance for any responses.  And happy holidays to us all.
> 
> Tom Huxford.
> ==
> Tom Huxford.
> Structural Biochemistry Laboratory
> Department of Chemistry & Biochemistry
> San Diego State University
> (619) 594-1606
> 

Re: [ccp4bb] Crystal with ZERO diffraction

[Keller, Jacob]

>In a second case we were working on a beamline on the west coast of the US. 
>Every crystal we put on vanished before we could even collect data - the loops 
>appeared empty as soon as we looked through the microscope (this sets the 
>decade). The beamline had an extra strong magnet on the goniometer and on 
>closer inspection we saw that the hutch wall next to the goniometer was 
>peppered with many crystals - they were being catapulted out of the loop when 
>the base 'flipped' onto the magnet. There were so many that others will know 
>this beamline.

Yes, I also catapulted some crystals-but I actually saw one of mine fly off the 
loop

JPK

Re: [ccp4bb] Crystal with ZERO diffraction

[Edward Snell]

Hi Tom et al.,

While probably unrelated, as a fresh graduate student we did one experiment 
where we observed no diffraction signal at all - no beamstop shadow, solvent 
ring etc. Being clever (we thought), we ran burn paper from the slits into the 
hutch, then through the hutch step by step along the path, to the detector 
position. We confirmed that the beam was indeed aligned, and when the beamstop 
was removed, that the beam was getting to the large sheet of lead in front of 
the detector. It was at that point, that the problem become obvious. We still 
have about two centuries of burn paper left in the cold room!

In a second case we were working on a beamline on the west coast of the US. 
Every crystal we put on vanished before we could even collect data - the loops 
appeared empty as soon as we looked through the microscope (this sets the 
decade). The beamline had an extra strong magnet on the goniometer and on 
closer inspection we saw that the hutch wall next to the goniometer was 
peppered with many crystals - they were being catapulted out of the loop when 
the base 'flipped' onto the magnet. There were so many that others will know 
this beamline.

Both are probably unrelated to what you observed, some crystals are just ghost 
crystals, a term coined by George DeTitta I think. I'd love to know why myself.

If all else fails, grow more crystals - shameless plug http://getacrystal.org

A wonderful holiday season to all and may the new year be full of strongly 
diffracting crystals and plenty of X-rays.

Best wishes,

Eddie


Edward Snell Ph.D.
President and CEO Hauptman-Woodward Medical Research Institute
Assistant Prof. Department of Structural Biology, University at Buffalo
700 Ellicott Street, Buffalo, NY 14203-1102
http://hwi.buffalo.edu
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
[cid:image001.png@01D25B9C.BD1AC640]
Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom 
Huxford
Sent: Wednesday, December 21, 2016 2:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Crystal with ZERO diffraction

Dear ccp4b collective mind and experience,

Greetings from San Diego.

I have done my fair share of synchrotron data collection on many diverse 
macromolecular crystal systems.  But this weekend was the first time that I 
ever shot crystals that failed to diffract entirely.

Details:  we have purified and crystallized an ~90 kDa proteolytic fragment 
containing a single point mutant version of a myosin motor domain in complex 
with a separate light chain polypeptide.  The crystals are relatively small 
(10-30 microns in each dimension) but clearly crystalline in character (clear 
faces, edges, and facets).  The crystals tested positive for protein by 
absorbance at 280 nm.  This weekend we tested more than 40 of them for 
diffraction in different cryo solvents and did not observe a single 
identifiable diffracted ray.  It was as if we had only cryo on the end of our 
loops.  Increasing the time of exposure or annealing did nothing to improve the 
situation.  Crystals from a different protein system that we also tested this 
weekend on the same beamline diffracted to beyond 1.3 Å.

I only post this because, in my experience, crystals of this size and 
superficial quality always give some signal--even if it is horrifyingly bad.  
But never complete diffraction silence.  We will work this week to identify 
what it is that we "crystallized".  But can anybody who has had a similar 
experience suggest what it is that could be going on here?

Thanks in advance for any responses.  And happy holidays to us all.

Tom Huxford.
==
Tom Huxford.
Structural Biochemistry Laboratory
Department of Chemistry & Biochemistry
San Diego State University
(619) 594-1606

[ccp4bb] Crystal with ZERO diffraction

[Tom Huxford]

Dear ccp4b collective mind and experience,

Greetings from San Diego.

I have done my fair share of synchrotron data collection on many diverse 
macromolecular crystal systems.  But this weekend was the first time that I 
ever shot crystals that failed to diffract entirely.

Details:  we have purified and crystallized an ~90 kDa proteolytic fragment 
containing a single point mutant version of a myosin motor domain in complex 
with a separate light chain polypeptide.  The crystals are relatively small 
(10-30 microns in each dimension) but clearly crystalline in character (clear 
faces, edges, and facets).  The crystals tested positive for protein by 
absorbance at 280 nm.  This weekend we tested more than 40 of them for 
diffraction in different cryo solvents and did not observe a single 
identifiable diffracted ray.  It was as if we had only cryo on the end of our 
loops.  Increasing the time of exposure or annealing did nothing to improve the 
situation.  Crystals from a different protein system that we also tested this 
weekend on the same beamline diffracted to beyond 1.3 Å.

I only post this because, in my experience, crystals of this size and 
superficial quality always give some signal--even if it is horrifyingly bad.  
But never complete diffraction silence.  We will work this week to identify 
what it is that we "crystallized".  But can anybody who has had a similar 
experience suggest what it is that could be going on here?

Thanks in advance for any responses.  And happy holidays to us all.

Tom Huxford.
==
Tom Huxford.
Structural Biochemistry Laboratory
Department of Chemistry & Biochemistry
San Diego State University
(619) 594-1606

Re: [ccp4bb] Atom clashes in active site?

[Scott Horowitz]

Hi Andrew,

Here are those references:

for CH...O hydrogen bonds I'd recommend our review: "Carbon-Oxygen Hydrogen
Bonding in Biological Structure and Function" (2012)
http://www.jbc.org/content/287/50/41576.full

for chalcogen bonds, I don't know of a great recent review, but this recent
article (2016) has a whole bunch of references (listed under 19 and 20) on
it: https://www.ncbi.nlm.nih.gov/pubmed/27992115

Scott

On Tue, Dec 20, 2016 at 8:45 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:

> Hi Scott,
>
> That would be great if you have some references handy?
> Thanks very much,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
> On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz 
> wrote:
>
>> Hi Andrew,
>>
>> Based on the atoms and distances you are mentioning, these don't sound
>> like steric clashes, but like a chalcogen bond between the S and O atoms,
>> and CH...O hydrogen bonds between the O and CH3. These are common and
>> well-accepted interactions, but unfortunately aren't usually treated as
>> such by refinement programs. Let me know if you want references for these
>> interaction types.
>>
>> Scott
>>
>> On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall <
>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>
>>> Hi all,
>>>
>>> Thank you for your suggestions. I tried the pdb file edit (making the
>>> offending atoms of both the ligand and the protein 'B' altconf), but it
>>> didn't seem to make any difference to their positions after a single round
>>> of refinement..?
>>> The atoms in the active site concern two acetyl groups - one from the
>>> substrate, acetyl-CoA, and the other from an acetylated cysteine in the
>>> protein - that I believe are poised ready for a condensation reaction. The
>>> closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3
>>> (3.1A), but going off the density, I think these should be closer (more
>>> like 2.8 or 2.7A). It may be that I've trapped another reaction
>>> intermediate (which would be cool), but I don't think that fits the density
>>> quite as well. Any thoughts/ideas?
>>>
>>> Thanks,
>>>
>>> Andrew Marshall
>>> PhD Candidate
>>> Laboratory of Protein Crystallography
>>> Dept. of Molecular and Cellular Biology
>>> School of Biological Sciences
>>> The University of Adelaide
>>>
>>> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz 
>>> wrote:
>>>
 Hi Andrew,

 I'm curious- what are the atoms that are clashing? I worked on this
 sort of thing back in my Ph.D., and so I might have some useful tidbits if,
 for example, the S is clashing with a carbon of some sort.

 Thanks,
 Scott

 On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall <
 andrew.c.marsh...@adelaide.edu.au> wrote:

> Hi all,
>
> I have a structure of a condensing enzyme with substrate bound. The
> active site is very tight, requiring some of the substrate atoms to clash
> with a catalytic cysteine. This means that although the substrate fits the
> density nicely upon manual real-space refinement, phenix recognises the
> clash, resulting in the displacement of substrate atoms so that they are
> outside the density. I can mostly fix this by using distance restraints,
> but I'd rather allow it to refine in a less biased manner, but ignore the
> clash. Is this a acceptable way forward? If so, is there a parameter I can
> edit to tell phenix to ignore clashes between these specific atoms?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
>


 --
 Scott Horowitz, Ph.D.
 Postdoctoral Fellow

 University of Michigan
 Department of Molecular, Cellular, and Developmental Biology
 Bardwell lab
 830 N. University Ave, Room 4007
 Ann Arbor, MI 48109
 phone: 734-647-6683
 fax: 734-615-4226

>>>
>>>
>>
>>
>> --
>> Scott Horowitz, Ph.D.
>> Postdoctoral Fellow
>>
>> University of Michigan
>> Department of Molecular, Cellular, and Developmental Biology
>> Bardwell lab
>> 830 N. University Ave, Room 4007
>> Ann Arbor, MI 48109
>> phone: 734-647-6683
>> fax: 734-615-4226
>>
>
>


-- 
Scott Horowitz, Ph.D.
Postdoctoral Fellow

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
phone: 734-647-6683
fax: 734-615-4226

[ccp4bb] Postdoc position available at Emory University, Atlanta GA, USA

[Conn, Graeme L]

A postdoctoral position at Emory University is available immediately on an 
NIH-funded project investigating bacterial antibiotic-resistance ribosomal RNA 
methyltransferases. We use interdisciplinary approaches including structural 
biology, biochemistry, molecular biology and microbiology to address molecular 
mechanistic questions related to the activities of these antibiotic resistance 
determinants from both drug-producing and human pathogenic bacteria. The 
position is part of an on-going collaborative project between the groups of 
Drs. Graeme L. Conn and Christine M. Dunham, both located in the Department of 
Biochemistry, Emory University School of Medicine in Atlanta GA, USA. For more 
information on this project and recent publications please see:

http://www.biochem.emory.edu/conn

http://www.biochem.emory.edu/dunham

The Emory Department of Biochemistry has state-of-the-art shared facilities for 
crystallization and in-house X-ray data collection as well as providing regular 
synchrotron beamtime at the Advanced Photon Source (APS) through our membership 
of SER-CAT. Outstanding facilities for complementary biophysical approaches 
(e.g. HDX-MS, ITC, SPR, etc) are also available through the Emory integrated 
core facilities. Additionally, both labs have been at the forefront of 
developing the infrastructure for high-resolution single particle cryo-EM on 
the Emory campus (from 2017) which will be applicable to this project. We are 
also part of the Emory Antibiotic Resistance Center (ARC; see 
http://www.antibiotics.emory.edu/) which provides a diverse and intellectually 
stimulating environment for research and practice related to all aspects of 
bacterial antibiotic resistance.

Interested applicants should have a Ph.D. in biochemistry, molecular biology or 
structural biology, and, ideally, experience in X-ray crystallography and/ or 
high-resolution single particle cryo-EM. The ideal candidate will be highly 
motivated, possess excellent communication skills and the ability to work in a 
collaborative, team-oriented environment.

To apply, please e-mail a CV including a list of publications, a brief 
statement of experience and scientific interests, and contact information for 
three references to gc...@emory.edu.

_

Graeme L. Conn, Ph.D.
Department of Biochemistry
Emory University School of Medicine
1510 Clifton Road NE - Room 4135
Atlanta GA 30322 USA

E.mail gc...@emory.edu
Office (404) 727-5965
Lab (404) 712-0058
FAX (404) 727-2738
Lab Webpage
ORCiD
_







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[ccp4bb] SeMet in S2 cell

[Xianchi Dong]

Dear All,

Does anybody have experience with SetMet protein in S2 cells? What kind of
reagent should I use and is anything else I should pay attention to?
Thanks in advance.

Best,
Xianchi

[ccp4bb] PhD studentships at Universiy of Leicester

[Peter Moody]

The newly founded (and exceptionally wonderful)  Leicester Institute for
Structural & Chemical Biology has funded PhD studentships available for
September 2017 start

Please see

http://www2.le.ac.uk/institutes/liscb/study-at-liscb





We also members of
the *M*idlands *I*ntegrative *B*iosciences* P*artnership, the home page is

http://www2.warwick.ac.uk/fac/cross_fac/mibtp/


Suitably brilliant candiates with an addiction to high-risk and wish for
obscurity might like to look at
http://www2.warwick.ac.uk/fac/cross_fac/mibtp/pgstudy/phd_opportunities/molecular2017/neutron




Compliments of the season, Peter


PS please do not reply to this email address, the popularity of CCP4BB
means thing get lost.

[ccp4bb] iNEXT course: “X-ray and neutron diffraction studies of macromolecules: from data collection to structures” (Oulu, Finland, May-15 to May-19, 2017)

[Rikkert Wierenga]

Dear All,

We are pleased to announce our iNEXT course: “X-ray and neutron diffraction 
studies of macromolecules: from data collection to structures”. This intensive 
course is organized from May-15 to May-19, 2017 at the Faculty of Biochemistry 
and Molecular Medicine, University of Oulu in Oulu, Finland. It is organized in 
the context of the iNEXT Horizon2020 project (http://www.inext-eu.org ), 
together with Diamond (Oxford, UK) and Biocenter Oulu. The course will include 
an introduction on the methods of protein crystallography (Rupp), neutron 
crystallography (Oksanen/Podjarny) and SAXS/SANS-approaches (Svergun). Also 
data collection at synchrotrons (Thunnissen), new perspectives when using the 
new long-wavelength beamline at Diamond (Wagner) and when using XFEL-technology 
(Hajdu) will be addressed. Tutorials include the validation tools of the 
PDB-deposition server (Rupp), as well as data processing (DIALS, Waterman; XDS, 
Rower), experimental phasing (SHELX, Gruene), molecular replacement phasing 
(CCP4, Lebedev) and neutron structure refinement (Oksanen, Podjarny). Remote 
data collection (Diamond, Aller, Powell) of crystals from participating 
students is scheduled for the last day of the course. The course provides 
extensive opportunities for the students to work with the presented software in 
our linux class room and to interact with the expert teachers.

Students are encouraged to send crystals in advance, which will then be shipped 
to Diamond, for remote X-ray data collection. Students are also encouraged to 
bring their own raw X-ray data images which are difficult to process or their 
own X-ray data sets for which molecular replacement calculations have turned 
out to be difficult.

There is no registration fee and we aim to cover also the accommodation costs 
and meals of the students. Application for the course can be sent in January 
and the deadline is 31.01.2017. The course is aimed at PhD-students and 
postdocs working on structural biology projects using X-ray or neutron 
diffraction methods.  The application should include a motivation letter and a 
letter from the supervisor. Detailed information on how to apply, including a 
list of confirmed lectures and tutorials, is available at 
http://www.oulu.fi/biocenter/instruct-nac/courses/oulu .

On behalf of the local organisers,
Rik Wierenga and Lari Lehtiö