[ccp4bb] General interest

[John R Helliwell]

Dear Colleagues,
For your general interest, you can find the lecture slides that I presented at 
ACA 2019 in the Transactions Symposium on Data via the weblink here:-
https://forums.iucr.org/viewtopic.php?f=39=421 
Best wishes,
John 
Emeritus Professor John R Helliwell DSc
Chairman of IUCr CommDat 





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Re: [ccp4bb] challenges in structural biology

[Gloria Borgstahl]

Sorry to be late chiming in on this post (survived RAGBRAI).  I think the
challenges (crystallization, perdeuteration) and benefits of neutron
crystallography (where are those protons) could be included.  We are now in
an era of using cryotrapping with neutrons which I think is really cutting
edge for time-resolved structural information.  My two cents, G

On Mon, Jul 22, 2019 at 1:55 AM Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Dear Artem, Tom, Janet,
>
> for me and probably others the usage of words like 'magic bullet' (which
> you defend, or try to redefine) implies a belief-based esoteric approach
> that has little to do with science. I suggest that to obtain funding,
> 'magic bullets' should not be promised, because these cannot be delivered
> (I gave the lo-gravity hi-funding example).
>
> That this discussion (including messages by Janet and Tom) happens at all
> suggests that crystallization is currently not a science - it lacks a
> consistent nomenclature and way of documentation, and suffers from strong
> publication bias (many unpublished negative results).
>
> On the other hand, what you (Janet, Tom) write about the research that
> should/could be performed - this sounds a lot like a scientific approach,
> and is not different from what has been realized in other areas of
> crystallography. Yes, existing tools for predicting crystallization success
> are not consulted because the rate of false positives and false negatives
> is high. If those rates could be reproducibly reduced, I bet the usage
> would go up - that could start a feedback loop leading to even better
> predictions. Is work in this direction sexy? No. Is it useful? Yes. Is it
> hard work? Yes. Does it contribute to make crystallization a science? Yes.
>
> What about 'deep learning' applied to crystallization outcomes? Can it
> guide individual trials better than intuition? Can it find previously
> unknown promising combinations on a larger scale?
>
> Can this be funded? Yes of course. Your statement that crystallization
> gets no funding may be true in some countries (but aren't CCP4BB readers
> from the U.S. also reviewers?), but it's untrue in others - think of groups
> in France that obviously got long-term funding. And for space (low-gravity)
> - that amount of funding could have been used for a lot of meaningful
> earth-bound research.
>
> Kay
>
>
> Am 21.07.19 um 23:04 schrieb Artem Evdokimov:
> > Dear Kay
> >
> >
> > I disagree that 'magic bullet' is impossible. I think the definition is
> wrong here - magic bullet to me is a rational set of methods that (when
> executed with precision and care) enable crystallization to the maximum
> possible benefit. This includes everything - constructs, crystallization
> design, etc. Part of the magic bullet is also a precise knowledge when
> crystallization is unlikely (i.e. an actual proven predictor that
> consistently discriminates between "you're going to succeed if you work
> hard" and "it's doomed to fail, don't bother" scenarios in crystallization.
> >
> > The above is not sexy. It does not present itself as a lovely subject on
> which to have international cocktail parties with politicians delivering
> fancy speeches. But that is what is needed, and no one is funding that to
> the best of my knowledge.
> >
> > What needs to be done is a significant amount of testing,
> standardization, and methods development from the perspective of holistic
> outcome (i.e. crystals that work) - and none of the previously advertised
> 'magic bullets' work the way I just described.
> >
> > Having written this, I think you're right - this is a bit of a
> distraction from James' original point. However it's a valid opportunity
> for a lively discussion on its own :)
> >
> > Artem
> >
> > - Cosmic Cats approve of this message
> >
> >
> > On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs <
> kay.diederi...@uni-konstanz.de >
> wrote:
> >
> > Dear Artem,
> >
> > black or white is not my way of thinking, which is why I don't
> believe in Hannibal's approach when it comes to crystallization.
> >
> > None of the magic bullets that were advertised over the past decades
> have proven generally applicable.  I believe more in incremental
> improvement which in this case includes a few biophysical characterization
> methods, possibly improved microfluidics or other apparatus, and expanded
> screens. And a lot of hard work, perseverance, intuition, frustration
> >  tolerance. Nothing that really needs huge funding - of course it
> does need money, but just a  share of what is anyway needed for the usual
> lab work including expression, purification, functional characterization,
> binding studies and the like.
> >
> > One area where a huge amount of money was burnt is crystallization
> in space, on board of e.g. the spacelab and ISS. This is for me an example
> of a mis-led approach to throw money at a difficult problem, with the
> 

Re: [ccp4bb] cbf to sfrm

[Andreas Förster]

Dear Tim and all,

if anyone is interested in converting EIGER HDF5 files directly to Bruker
format (SFRM), please contact me.  There's no need to go via CBF or similar
intermediaries.

All best.


Andreas



On Sun, Jul 28, 2019 at 12:25 PM Tim Gruene  wrote:

> Dear all,
>
> recently the conversion from CBF to SFRM frame format with APEX was
> discussed
> on the Bruker mailing list ("Synchrotron data with Bruker Software"),
> including a potential bug that parameters in the frames other than the
> first
> frame are not set correctly. The workaround to re-convert from SFRM to
> SFRM a
> second time did not help in my case.
>
> I therefore updated my program sfrmtools, available at https://
> homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/
>
> With the option '-u',you can provide the first frame of the run, and via
> '-p'
> a parameter file that contains the critical parameters (see documentation
> at
> above URL) to update the header for all frames in this run. In case you
> have
> twinned data and want to benefit from SAINT, this should be possible with
> this
> feature.
>
> Both 64bit Linux binary and the source code are available. The program has
> no
> dependencies and should compile under any platform.
>
> I did not debug this new feature very thoroughly, but it worked for me so
> far.
> Any bug reports are welcome to this address tim.gru...@univie.ac.at
>
> I hope this is helpful for one or two users.
>
> I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM
> header format.
>
> Kind regards,
> Tim
>
> cc Bruker mailing list, CCP4BB, phenixBB
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
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>


-- 

Andreas Förster, Ph.D.
Application Scientist Crystallography
Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com







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[ccp4bb] ISOLDE dev builds now available

[Tristan Croll]

Hi all,

Since the release of ISOLDE 1.0b3 I've begun releasing regular 
(weekly~fortnightly) development builds of ISOLDE. These are built 
against the ChimeraX daily build at the time of release - if you 
download a ChimeraX-daily build and install ISOLDE in the usual way via 
Tools/More Tools... this is what you'll get. In case you're worried, the 
dev and official 1.0b3 builds install into different directories, so 
it's quite straightforward to have both versions running independently 
on the same machine. The dev builds are *not* compatible with the 
ChimeraX 0.9 stable release.


Some important changes since 1.0b3/ChimeraX 0.9:

- the ChimeraX team have fixed some bugs affecting PDB and mmCIF I/O 
(primarily involving the handling of "imperfect" files)
- fixed a bug causing the simulation to crash if the minimiser didn't 
converge in the first round
- added status messages during simulation startup, and clear indications 
of when a simulation is running/paused
- improved simulation startup time, and handling of custom ligands 
(preparing ligand definition files is a work in progress and will 
currently need you to do some work outside ISOLDE - feel free to contact 
me if you have an urgent case)


Best regards,

Tristan



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[ccp4bb] Postdoc and PhD position in Oxford

[Christian Siebold]

Dear all

 

We are looking for a Postdoctoral Research Scientist and a PhD student to join 
our group at the Division of Structural Biology (STRUBI), University of Oxford, 
UK. Research in the Siebold group is focused on the structural biology of 
mammalian cell surface signalling pathways involved in embryonic development 
and neuronal guidance (see e.g. Byrne et al Nature 2016, Healey et al NSMB 
2015, Bell et al Science 2013). The work will involve the structural analysis 
(cryo-EM and X-ray crystallography) of membrane proteins and extracellular 
signalling assemblies, and assessment of these in the context of normal and 
disease-associated signalling. Deadline is 12th August 2019. More information 
can be found here:

 
Postdoc link:
https://www.ndm.ox.ac.uk/current-job-vacancies/vacancy/141505-Postdoctoral-Research-Scientist-in-cryo-EM
 
PhD link:
https://www.findaphd.com/phds/project/cancer-research-uk-phd-studentship-molecular-mechanisms-of-cell-surface-morphogen-signalling/?p110933
 
Please do not hesitate to contact me, if you have additional questions.
 
Best wishes,
Christian




Christian Siebold, PhD
Professor of Structural Biology

University of Oxford
Wellcome Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive, Oxford OX3 7BN
United Kingdom
Email: christ...@strubi.ox.ac.uk
Phone: (+44)-1865-287564
http://www.strubi.ox.ac.uk/research/christian-siebold 




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Re: [ccp4bb] challenges in structural biology

[CCP4BB]

Hi

It's pretty much what the powder people do when using Rietveld refinement, 
isn't it? As far as I know, they fit a calculated curve from their structure to 
a 1D trace of the powder pattern (happy to be corrected on this). All you need 
to do is extend this to 3D - there may be enough work there for a project 
student ;-).

Harry
--
Dr Harry Powell

> On 30 Jul 2019, at 10:47, Loes Kroon-Batenburg  
> wrote:
> 
> Dear Jacob,
> 
> That should indeed be our ultimate goal: refining against the image data 
> rather than against process data. This would require a good model for the 
> crystal, mosaicity being an important parameter in this, and for the internal 
> variation in the molecular structure. Modelling the Bragg spots is what we do 
> currently wth EVAL.  James Holton is doing also this with nanoBragg. 
> Unfortunately we would also have to simulate solvent rings etc. 
> 
> Best wishes,
> Loes
>> On 07/25/19 19:07, Keller, Jacob wrote:
>> >>It would seem to me that an important issue is also: do get all 
>> >>information out of our diffraction data? By integrating the Bragg peaks we 
>> >>usually neglect the diffuse scattering that could potentially contain 
>> >>additional (dynamic) structural information. This can be cloudy diffuse 
>> >>scattering hidden in the background but also diffuse streaks that contain 
>> >>information on packing disorder and reveals intrinsic interactions in the 
>> >>crystal.
>> 
>> Along these lines, and taking a page from you also, how about 
>> “crystallographic model refinement as image-faking?” Metrics of the goodness 
>> of a particular refinement could simply be some measure of the correlation 
>> between predicted vs. measured images. I have seen some of this done with 
>> diffuse scattering, but why not with the whole thing, including intensity 
>> and shape of Bragg peaks, solvent rings, etc? Maybe instead of doing the 
>> multiple steps of (indexing, integration, scaling, solving…) all of this 
>> could be refined as one? Processing parameters like moscaicity [sic] etc 
>> would now be part of the final model…?
>>  
>> JPK
>>  
>>  
>>  
>> 
>> Loes Kroon-Batenburg
>> 
>> On 07/15/19 21:44, Holton, James M wrote:
>> Hello folks,
>>  
>> I have the distinct honor of chairing the next Gordon Research 
>> Conference on Diffraction Methods in Structural Biology (July 26-31 
>> 2020).  This meeting will focus on the biggest challenges currently 
>> faced by structural biologists, and I mean actual real-world 
>> challenges.  As much as possible, these challenges will take the form of 
>> friendly competitions with defined parameters, data, a scoring system, 
>> and "winners", to be established along with other unpublished results 
>> only at the meeting, as is tradition at GRCs.
>>  
>> But what are the principle challenges in biological structure 
>> determination today?  I of course have my own ideas, but I feel like I'm 
>> forgetting something.  Obvious choices are:
>> 1) getting crystals to diffract better
>> 2) building models into low-resolution maps (after failing at #1)
>> 3) telling if a ligand is really there or not
>> 4) the phase problem (dealing with weak signal, twinning and 
>> pseudotranslation)
>> 5) what does "resolution" really mean?
>> 6) why are macromolecular R factors so much higher than small-molecule ones?
>> 7) what is the best way to process serial crystallography data?
>> 8) how should one deal with non-isomorphism in multi-crystal methods?
>> 9) what is the "structure" of something that won't sit still?
>>  
>> What am I missing?  Is industry facing different problems than 
>> academics?  Are there specific challenges facing electron-based 
>> techniques?  If so, could the combined strength of all the world's 
>> methods developers solve them?  I'm interested in hearing the voice of 
>> this community.  On or off-list is fine.
>>  
>> -James Holton
>> MAD Scientist
>>  
>>  
>> 
>>  
>> To unsubscribe from the CCP4BB list, click the following link:
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>> 
>> 
>> 
>> -- 
>>  
>> __
>>  
>> Dr. Loes Kroon-Batenburg
>> Dept. of Crystal and Structural Chemistry
>> Bijvoet Center for Biomolecular Research
>> Utrecht University
>> Padualaan 8, 3584 CH Utrecht
>> The Netherlands
>>  
>> E-mail : l.m.j.kroon-batenb...@uu.nl
>> phone  : +31-30-2532865
>> fax: +31-30-2533940
>> __ 
>>  
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
> 
> 
> -- 
> 
> __
> 
> Dr. Loes Kroon-Batenburg
> Dept. of Crystal and Structural Chemistry
> Bijvoet Center for Biomolecular Research
> Utrecht University
> Padualaan 8, 3584 CH Utrecht
> The Netherlands
> 
> E-mail : l.m.j.kroon-batenb...@uu.nl
> phone  : +31-30-2532865
> 

[ccp4bb] Postdoc in DNA Repair Structural Biology

[Laurence Pearl]

A Post-doctoral position funded by Cancer Research UK is available from 1st 
October 2019 in the laboratory of Prof. Laurence Pearl FRS and Dr. Antony 
Oliver, in the Genome Damage and Stability Centre at the University of Sussex, 
to study the structure and mechanism of multi-protein complexes involved in the 
recognition and repair of DNA single-strand breaks and gaps, primarily using 
single particle reconstruction by cryo-electron microscopy.

https://www.sussex.ac.uk/about/jobs/post-doctoral-research-fellow-structural-biology


Laurence H. Pearl PhD FRS FMedSci

Professor of Structural Biology
Genome Damage and Stability Centre
University of Sussex, Brighton, BN1 9RQ, UK

Phone +44-(0)1273  678 349

"Live Modestly and do Serious Things .. "
- Dorothy Crowfoot Hodgkin






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