[ccp4bb] Machine Learning researcher position at Uppsala University

[Annette Roos]

Dear all,


Uppsala University and Science for Life Laboratory is looking to hire a 
chemoinformatician.


Please spread to those who may be interested. Sweden had some nice publicity at 
the CCP4 Study Weekend ;) and Uppsala can today offer a substantial amount of 
fluffy snow.



The applicant is to identify and implement relevant methods in machine learning 
to support drug discovery projects. We work with small molecule and 
oligonucleotide drug discovery as well as protein-based therapeutics.


The position will be very collaborative.



https://www.jobb.uu.se/details/?positionId=697784



best wishes,


Annette


---
Annette Roos, PhD
Head of Biophysical Screening and Characterization Unit
SciLifeLab Drug Discovery and Development Platform,
ICM, Box 596, Uppsala University
751 24 Uppsala,
Sweden
https://www.scilifelab.se/platforms/ddd









När du har kontakt med oss på Uppsala universitet med e-post så innebär det att 
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du 
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

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[ccp4bb] Call for proposals at MAX IV

[Ana Gonzalez]

The 4th generation synchrotron source MAX IV welcomes  beamtime proposals for 
BioMAX, FragMAX, MicroMAX and CoSAXS.


BioMAX and MicroMAX are dedicated macromolecular  crystallography beamlines. 
BioMAX is capable of a wide array of techniques, from high throughput 
conventional oscillation experiments to serial crystallography. BioMAX also 
hosts FragMAX, a fragment-based drug discovery platform and has no time 
limitations for proprietary research.

MicroMAX is ideally suited for microfocus applications, serial crystallography 
and time-resolved experiments. In this call, MicroMAX is open for serial and 
time-resolved crystallography as well as automated single-crystal 
crystallography.

The CoSAXS beamline is a state-of-the-art multipurpose Small Angle X-ray 
Scattering  (SAXS) instrument offering protein solution and time resolved SAXS 
amongst other techniques.

Proposal application deadline:  March 6th  2024 14:00 CET
Beamtime period: Sep 2024 - March 2025
Proposal submission:
https://www.maxiv.lu.se/user-access/user-guide/proposal-submission/

BioMAX:
https://www.maxiv.lu.se/beamlines-accelerators/beamlines/biomax/

FragMAX:
https://www.maxiv.lu.se/beamlines-accelerators/science-initiatives/fragmax-biomax-fragment-screening-platform/

MicroMAX:
https://www.maxiv.lu.se/beamlines-accelerators/beamlines/micromax/

CoSAXS:
https://www.maxiv.lu.se/beamlines-accelerators/beamlines/cosaxs/

Contacts:
Ana Gonzalez ana.gonza...@maxiv.lu.se  (BioMAX)
Tobias Krojer tobias.kro...@maxiv.lu.se  (FragMAX)
Thomas Ursby thomas.ur...@maxiv.lu.se  (MicroMAX)
Ann Terry ann.te...@maxiv.lu.se  (CoSAXS)




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[ccp4bb] Fwd: Open Position (tenure track) - Scientist in Neutron Spectroscopy - at PSI/LNS

[Schertler Gebhard]

Prof. em. Gebhard F.X. Schertler
Strukturbiologie ETH Zürich

ERC Investigator
Head of Biology and Chemistry
Division
Paul Scherrer Institut
OSRA 007
CH-5232 Villigen PSI
gebhard.schert...@psi.ch
phone +41 56 310 4265

Anfang der weitergeleiteten Nachricht:

Von: PSI User Office 
Datum: 13. Februar 2024 um 09:24:19 MEZ
An: Schertler Gebhard 
Betreff: Open Position (tenure track) - Scientist in Neutron Spectroscopy - at  
PSI/LNS

There is an open tenure track position for a Scientist in Neutron Spectroscopy 
within the "Solid State Dynamics Group" (Laboratory for Neutron Scattering and 
Imaging, LNS) at the Paul Scherrer Institute, Villigen, Switzerland.

Further information and online application:
https://www.psi.ch/en/pa/job-opportunities/61678-scientist-in-neutron-spectroscopy

Contact:
Dr Christof Niedermayer, email: christof.niederma...@psi.ch, phone: 
+41-56-310-2086

Application deadline:
13 March 2024

Paul Scherrer Insitut, Human Resources Management, Sevil Miniti, 5232 Villigen 
PSI, Switzerland


We apologize for multiple receipt of this posting!


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[ccp4bb] PhD position in the group of Titia Sixma at the Netherlands Cancer Institute in Amsterdam

[Titia Sixma]

A 4-year PhD position is available in the group of Titia Sixma at the 
Netherlands Cancer Institute in Amsterdam to study human DNA mismatch repair 
using cryo-EM and quantitative biochemistry 
(https://www.nki.nl/research/research-groups/titia-sixma/ ).

The project is part of the RepState project 
(www.repstate.eu ), where we study defined states of 
human DNA mismatch repair proteins, structurally, biochemically and 
biophysically. Applications can be made directly to Titia Sixma 
(t.si...@nki.nl); considered motivation, cv and 3 references to 
t.si...@nki.nl. Deadline for application is March 2nd, 
2024.

Marie Curie projects involve close collaboration with partner labs and 
industrial partners. The Netherlands Cancer institute is an international 
center of excellence with a high standard of biological research and 
outstanding research facilities, with an interactive atmosphere. It is located 
in Amsterdam, with all its cultural amenities, close to the Schiphol airport. 
We share labspace and equipment with Anastassis (Tassos) Perrakis and Robbie 
Joosten, ensuring a lively structural biology community.

The project follows EU mobility rules: This means that the candidate must not 
have resided or carried out their main activity (work, studies etc) in the 
Netherlands for more than 12 months in the 36 months immediately before the 
recruitment date (=first day of employment). A master degree in the life 
science is required, experience with protein purification and/or structural 
biology highly preferred. Deadline is March 2, 2024.







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Re: [ccp4bb] About Staraniso

[Gerard Bricogne]

Dear Kay,

 I think I should add a few comments and annotations to your reply to
Arpita, as it was addressed not just to her but to the general readership of
the CCP4BB. This will involve introducing an extra level of interleaving,
which can get a bit unsightly but can hardly be avoided.

 Please see below.


On Mon, Feb 12, 2024 at 04:55:02PM +, Kay Diederichs wrote:
> Dear Arpita,
> 
> I'll try to answer below -
> 
> On Mon, 12 Feb 2024 13:57:28 +0530, Arpita Goswami  
> wrote:
> 
> >Dear all,
> >
> >Greetings to all! Apologies if the below query seems very naive!
> >
> >This is to query on the consensus to use Staraniso for pdb submission. We
> >have solved a structure previously at 2.3 A resolution. The same data
> >(after reindexing the diffraction images in autoPROC) and after
> >reprocessing by ellipsoidal scaling in Staraniso gave structure at ~2.16 A.
> >
> >The previously solved structure did not have significant anisotropy
> >according to Aimless, so anisotropic scaling was not performed that time.
> 
> Maybe different resolution cutoffs were used: previously the 
> data were cut a 2.3A (according to some rule, e.g. "cut at =2"), 
> now they are cut at ~2.16A (according to a different rule, e.g. "cut at 
> =1.5").
> 
> Alternatively, different programs were used for data processing, and for
> the processing by the one used previously, the rule said "you should cut at 
> 2.3A", and for the one used now, the same rule said "cut at ~2.16A".
> After all, different programs give different data!
> 
> Speaking of rules, there are different "schools of thought" concerning the 
> "best" or "correct" rule for finding the resolution cutoff. I don't want to 
> repeat 
> the arguments here. It is important to know that there exists an experimental 
> and practical way (called "paired refinement") to find a meaningful 
> resolution 
> cutoff, and this requires refinement of a model, and comparison of 
> (basically) 
> Rfree values. The CCP4 program for this purpose is called PAIREF.
> There is also a web server called PDB-REDO that does paired refinement with
> your data and model.

 Arpita may not have come across the arguments that you don't want to
repeat, so she may find it useful to peruse the following item in the CCP4BB
archive: 

   https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg54145.html

that provides a useful introduction to the content of your paragraph above.
In particular, her use of PAIREF as available from CCP4 or PDB-REDO would
give her a resolution cut-off as a *single* number: applying such a cut-off
would then get her back to the situation where either good data will be
discarded in the better-diffracting direction(s), or essentially pure noise
will be kept in the worse-diffracting one(s). So this would be a huge step
backward from the results she has been alluding to, where we happen to know
that the default STARANISO analysis shows that these tetragonal crystals
diffract to 2.526 A along a* and b*, and to 2.039 A along c*. Trusting
PAIREF to give a useful indication of a single-number resolution in this
situation would seem totally unrealistic.

 There has been a publication on the simultaneous use of PAIREF and
STARANISO, using verbatim (and without acknowledgement) the procedure that
was suggested in the archive e-mail cited above (paragraph starting with
"Quite the contrary:"), namely using datasets obtained by running STARANISO
with different cut-off values for the local average of I/sig(I) and applying
the PAIREF procedure to assess which one is the most appropriate, and then
taking the associated diffraction limits as being the *three* diffraction
limits of the dataset. This way, one preserves the benefits of the
anisotropy analysis and one simply tweaks the STARANISO cut-off threshold
around its default value (1.2) by specifying another value through a
command-line parameter provided for that purpose since the inception of the
program. The publication in question can be found at 

  https://journals.iucr.org/j/issues/2023/04/00/ap5049/index.html

The process of exploring different STARANISO thresholds is manually driven,
and none of the available versions of PAIREF offer that feature - so
directing Arpita towards them may not be to her advantage. Before investing
too much hope in this type of investigation, it should be noted that this
article concludes that 

 "Corrections for diffraction anisotropy using the STARANISO server [with a
 default cut-off of 1.2] and [its output] data dramatically improved the
 quality of the observed electron density maps. No differences were observed
 with the extension of data from [those obtained with a cut-off value of
 1.2] to [those obtained with a cut-off value of 0.5]".


> >The overall spherical completeness of Staraniso structure is low (~73%)
> >while Ellipsoidal completeness is ~94%. Parallel isotropic scaling gives
> >structure with 99.6% completeness (but 2.3 A resolution). The statistics (R
> >merge 

Re: [ccp4bb] About Staraniso

[Kay Diederichs]

Dear readers of CCP4BB,

for various reasons I don't feel inclined to reply to this.

I'm really sorry,
Kay

On Tue, 13 Feb 2024 15:25:03 +, Gerard Bricogne  
wrote:

>Dear Kay,
>
...



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[ccp4bb] Combating disinformation in science and other areas

[Focco van den Akker]

Dear all,



As fellow scientists specializing in structural biology, it's disheartening
to witness a decline in society's trust in science; perhaps many of you
have come across the remarkable book "The Deadly Rise of Anti-science: A
Scientist's Warning" by Dr. Peter Hotez. To help restore this trust, we
co-founded a non-profit and launched an educational app. If you are
concerned as well, please read on (the app even touches on structural
biology):



As you know, scientists and other fact-finding professions like journalism
currently face significant challenges. Our crucial work as reputable
sources and the scientific consensus we build can be readily undermined by
misinformation and conspiracy theories.



There is probably no bigger problem in today’s world than the battle
between facts and mis- and disinformation, a conflict that not only fuels
other large global struggles such as vaccine hesitancy and climate change
denial but also leads to societal division and its consequential
challenges. These dynamics collectively contribute to heightened stress and
suffering, both on individual and global scales.



It's unlikely that any of the world's biggest challenges can be solved as
long as people remain so easily swayed by misinformation and
disinformation. To address this pressing issue, we co-founded the
non-profit organization Knowledge Advances Inc., dedicated to educating
individuals on navigating the complex ecosystem of information and
misinformation. We assert that information of higher reliability is a basic
human need, akin to water, food, and shelter.



To initiate our efforts, we recently launched an app called *Advance: Life
training*. The app employs a comprehensive, active learning approach
through quizzes to teach users how to identify sources of higher
reliability, discern information of greater credibility, and understand
biases.



For additional details and to download the free *Advance: Life Train*ing
app, please visit our website: https://knowledgeadvances.org/



If our approach and app resonate with you, we kindly ask you to support us
by rating our application on the app stores and sharing this information
with your friends and colleagues.



Please feel free to contact us for further information or feedback.



Best regards,



Focco



Focco van den Akker, Ph.D.

President, Knowledge Advances Inc.

Associate Professor, Dept. Biochemistry, Case Western Reserve University

Email: focco.vandenak...@knowledgeadvances.org

https://knowledgeadvances.org/

https://case.edu/medicine/biochemistry/faculty/focco-van-den-akker



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Re: [ccp4bb] About Staraniso

[Arpita Goswami]

Dear all,

Good day. Thank you all for the very extensive discussions. Both on- and
off-list discussions were very helpful.

Thank you and a very happy Valentine's day to all..

Best regards,
Arpita


On Wed, Feb 14, 2024, 01:25 Kay Diederichs 
wrote:

> Dear readers of CCP4BB,
>
> for various reasons I don't feel inclined to reply to this.
>
> I'm really sorry,
> Kay
>
> On Tue, 13 Feb 2024 15:25:03 +, Gerard Bricogne <
> g...@globalphasing.com> wrote:
>
> >Dear Kay,
> >
> ...
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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