Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

[dbellini]

Hi Marco,

A few suggestions that I like to follow for MAD experiments:

Before everything, check you have at least about 1 SeMet per 100 
residues
Then before crystallisation check by MassSpec that SeMet is properly 
incorporated in your protein
After crystallisation collect first on the peak with (very) high 
redundancy and as little/gentle dose as possible
Collecting the other wavelengths should give you better starting 
phases/maps, which might be very helpful at your resolution of 2.8 
(especially if it is a very anisotropic 2.8...)


Automated pipelines are so good nowadays, if you collect good data they 
should solve it without problems (as long as your crystal is not 
suffering from other pathologies like twinning or pseudosymmtries).


Good luck!

D


On 2024-05-14 01:17, Marco Bravo wrote:

CAUTION: This email originated from outside of the LMB:
.-owner-ccp...@jiscmail.ac.uk-.
Do not click links or open attachments unless you recognize the sender
and know the content is safe.
If you think this is a phishing email, please forward it to
phish...@mrc-lmb.cam.ac.uk
--

Hello all,
I have a data collection trip next week and plan to collect data on
selenomethionine derivative crystals at the al831 beamline. Are there
any resources, tips, tutorials, literature etc. That you can recommend
to help me prepare for these experiments. Also is there a way to plug
in the experimental data into ccp4 cloud to do the automatic structure
solution? Do I need native and derivative data to solve the structure?
Last trip I collected a seemingly 2.8 angstrom resolution data on a
crystal of the native protein but could not get a solution depsite
extensive molecular replacement attempts. It seems that assigning a
space group for the crystals has been troublesome as well. here is my
last thread I posted about the issue for reference.

https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2402=CCP4BB=D=CCE6DFA19FA3D40346=mbrav005%40ucr.edu=112302



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Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility

[Paul Adams]

The letter may have had (or helped have) an impact already:

On X today from Pushmeet Kohli @ DeepMind

"We love the excitement & results from the community on AlphaFold 3 and are 
doubling the AF Server daily job limit to 20. Happy to also share that we're 
working on releasing the AF3 model (incl weights) for academic use, which 
doesn’t depend on our research infra, within 6 months".


> On May 13, 2024, at 11:11 AM, Wankowicz, Stephanie 
>  wrote:
> 
> If it does what it claims – incredibly impressive. The issue we have is there 
> is no way to verify or validate the claims it is making. 
> 
> The letter is a call and start of a conversation about how the ever-changing 
> landscape of communication and publication of science should be.
> 
> -Stephanie Wankowicz
> From: CCP4 bulletin board  > on behalf of Krieger, James M 
> mailto:krieg...@pitt.edu>>
> Sent: Monday, May 13, 2024 10:22 AM
> To: CCP4BB@JISCMAIL.AC.UK  
> mailto:CCP4BB@JISCMAIL.AC.UK>>
> Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility
>  
> This Message Is From an External Sender 
> This message came from outside your organization. 
> It definitely is impressive but it also has clear limitations
> 
>> On 13 May 2024, at 15:22, Sylvia Fanucchi 
>>  wrote:
>> 
>> 
>> You don't often get email from 
>> d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. Learn why this is important 
>> 
>>  
>> Is it just me who is really impressed by it? Am I missing something?
>> 
>> Get Outlook for Android 
>> 
>> From: CCP4 bulletin board  on behalf of Rafael 
>> Marques 
>> Sent: Monday, May 13, 2024 3:13:16 PM
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility
>>  
>> I tried it yesterday and I was really shocked by how fast it is. When I was 
>> preparing to submit my second job, the first one was already finished, which 
>> made me think that I was definitely doing something wrong. Probably I was...
>> 
>> Best wishes 
>> 
>> Rafael Marques 
>> 
>> 
>> On 13 May 2024 09:53, Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> Hi folks 
>> 
>> This arrived in my inbox this morning, and I believe that it may provoke 
>> some discussion…
>> 
>> Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν 
>> 
>> Best wishes! 
>> 
>> Harry 
>> 
>> >From: Stephanie Wankowicz  
>> >Sent: Saturday, May 11, 2024 3:31 PM 
>> >To: James Fraser ; Pedro Beltrao 
>> > ; Benjamin Cravatt ; Roland 
>> > Dunbrack ; Anthony Gitter 
>> > ; Kresten Lindorff-Larsen ; 
>> > Sergey Ovchinnikov ; Polizzi, Nicholas F. 
>> > ; Brian Shoichet 
>> >Subject: AlphaFold3 Transparency and Reproducibility 
>> > 
>> > 
>> >This email from mullane.stepha...@gmail.com originates from outside 
>> > Imperial. Do not click on links and attachments unless you recognise the 
>> > sender. If you trust the sender, add them to your safe senders list 
>> >  
>> > 
>> >  to disable email stamping for this address. 
>> > 
>> >Hello, 
>> > 
>> > 
>> >As many of you, we were incredibly disappointed with the lack of code 
>> > or even executables accompanying the publication of AlphaFold3 in Nature. 
>> > AlphaFold3 was released without the means to test and use the software in 
>> > a high-throughput manner. This does not align with the principles of 
>> > scientific research, which rely on the ability of the community to 
>> > evaluate, use, and build upon existing work.
>> > 
>> > 
>> > 
>> >We have written a letter, which will be posted on Zenodo and submitted 
>> > as a Letter to the Editor in the coming days.
>> > 
>> > 
>> > 
>> >Please see the entire letter here. 
>> > 
>> >  
>> > 
>> >  If you want to endorse this letter, please fill out your name, 
>> > affiliation, and email in the form.
>> > 
>> > 
>> > 
>> >Additionally, a PDF version of the letter can be found here 
>> > 

[ccp4bb] RES: [ccp4bb] What could these crystals be?

[Rafael Marques]

It seems to me that your drop has dried. By the pic, I would not say these are 
crystals

Best


Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester

Mestre em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"



De: CCP4 bulletin board  em nome de 张慧欣 

Enviado: Monday, May 13, 2024 3:15:09 PM
Para: CCP4BB@JISCMAIL.AC.UK 
Assunto: [ccp4bb] What could these crystals be?

Hi all
We have been trying with no success to crystalize a protein. Recently we got 
these strange shape "crystals". They are hard and flat . Any ideas as to what 
could cause this? The crystallization conditions is:0.06M Divalents  0.1M 
BICINE 0.1M Tris pH8.5  20% Ethylene glycol  10% PEG8000




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[ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

[Marco Bravo]

Hello all, 
I have a data collection trip next week and plan to collect data on 
selenomethionine derivative crystals at the al831 beamline. Are there any 
resources, tips, tutorials, literature etc. That you can recommend to help me 
prepare for these experiments. Also is there a way to plug in the experimental 
data into ccp4 cloud to do the automatic structure solution? Do I need native 
and derivative data to solve the structure? Last trip I collected a seemingly 
2.8 angstrom resolution data on a crystal of the native protein but could not 
get a solution depsite extensive molecular replacement attempts. It seems that 
assigning a space group for the crystals has been troublesome as well. here is 
my last thread I posted about the issue for reference. 

https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2402=CCP4BB=D=CCE6DFA19FA3D40346=mbrav005%40ucr.edu=112302



To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Tenure-track Assistant Professor position - Artificial Intelligence / Machine Learning

[Gagnon, Matthieu]

I would like to attract your attention to the following position that opens up 
at The University of Texas Medical Branch (UTMB).
Cheers.
Matt
​___

Assistant Professor - Artificial Intelligence / Machine Learning
The University of Texas Medical Branch (UTMB), Galveston, Texas, United States

https://aa083.referrals.selectminds.com/jobs/assistant-professor-microbiology-and-immunology-21011

Sealy Institute for Drug Discovery (SIDD) Faculty Opportunities 
(https://www.utmb.edu/sidd/home)
The newly established Sealy Institute for Drug Discovery seeks an outstanding 
bioinformatics expert for a tenure-track position at the rank of Assistant 
Professor at the University of Texas Medical Branch (UTMB), Galveston, Texas. 
Applicants meeting criteria for higher ranks will also be considered. The 
candidate is expected to have skills such as:

MINIMUM QUALIFICATIONS:

  *   PhD in Computer Science, Bioinformatics, Computational Biology, or a 
related field, with a strong emphasis on AI and machine learning.
  *   Postdoctoral or equivalent experience.
  *   A proven track record of research in applying AI to biological or 
chemical datasets with publications in peer-reviewed journals.
  *   Demonstrated ability to handle large (Big Data) datasets and experience 
with computational tools and databases relevant to genomics, proteomics, and 
drug discovery.
  *   Knowledge of biological and chemical data formats and standards, such as 
FASTA, FASTQ, BAM, VCF, BED, GFF, PDB, and SDF.
  *   Excellent communication and presentation skills, both oral and written.
  *   Strong problem-solving and critical thinking skills.
  *   Ability to work independently and collaboratively in a multidisciplinary 
and dynamic environment.
  *   High motivation and passion for bioinformatics and biomedical research.
  *   Strong theoretical understanding of key frameworks and AI model 
architectures


PREFERRED QUALIFICATIONS:

  *   Proficiency in Python and R as well as key frameworks for AI development 
(e.g. PyTorch, TensorFlow, JAX or equivalent).
  *   Familiarity with pipeline development and ability to work with teams to 
scale and operationalize new models and training regimes.
  *   Deep expertise in AI model development and an ability to extend and apply 
 tools such as AlphaFold, DiffDock, MolBert and similar tools in new and 
creative ways.
  *   Expertise in current model and paradigms such as transformers, graph 
neural networks, and embeddings.


Please submit complete application packets to Skott Harrington at 
sahar...@utmb.edu
UTMB is a world-class research center with strengths in infectious diseases, 
vaccine development, neuroscience, aging, and other disciplines.  In addition 
to a highly collaborative environment, UTMB offers outstanding research 
facilities for next-generation sequencing, mass spectrometry, optical 
microscopy, flow cytometry, solution biophysics, NMR, X-ray crystallography, 
cryo-electron microscopy, scientific computing, bioinformatics and deep 
computational resources, both locally and through the University of Texas 
system.  Excellent opportunities for scientific interactions exist through 
sister institutions in the Texas Medical Center and greater Houston area, Gulf 
Coast Consortia, and the Keck Center for Interdisciplinary Bioscience.

SALARY:
Commensurate with experience.

EQUAL EMPLOYMENT OPPORTUNITY:
UTMB Health strives to provide equal opportunity employment without regard to 
race, color, religion, age, national origin, sex, gender, sexual orientation, 
gender identity/expression, genetic information, disability, veteran status, or 
any other basis protected by institutional policy or by federal, state or local 
laws unless such distinction is required by law. As a VEVRAA Federal 
Contractor, UTMB Health takes affirmative action to hire and advance women, 
minorities, protected veterans and individuals with disabilities.



__

Matthieu G. Gagnon, Ph.D.

Assistant Professor

Department of Microbiology and Immunology

Adjunct Assistant Professor

Department of Biochemistry and Molecular Biology

Sealy Center for Structural Biology and Molecular Biophysics (SCSB)

Institute for Human Infections and Immunity (IHII)



The University of Texas Medical Branch
301 University Blvd., Galveston, TX 77555-1019

Medical Research Building, 4.104C

P (409) 772-2326 E magag...@utmb.edu


[cid:9a6b8efa-74db-4c47-9d42-156a90e3cf24]



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[ccp4bb] Early Career Diffraction Methods Seminar 2024 - reduced student fees and student grants available!

[Ali Ebrahim]

Dear CCP4BB,

A friendly reminder that Early Career Diffraction Methods Seminar 2024 is on 
the horizon! Taking place July 21-22, 2024 at The Harnack Haus, Berlin, this 
meeting is designed for early-career scientists to present and explore the 
latest advancements in diffraction methods, and engage with experts in the 
field. To register for a talk or poster presentation, and to view the full 
conference schedule, please visit https://events.gwdg.de/event/650/

The early career seminar precedes the highly anticipated Diffraction Methods in 
Structural Biology 2024 conference, running from July 22-27, 2024, and provides 
an excellent opportunity to showcase your work, receive valuable feedback, and 
connect with your peers.

Applications are still open and we invite you to submit abstracts for oral and 
poster presentations! Spaces are very limited and we hope to choose the seminar 
speakers from amongst the submitted abstracts by the first week of June.

We are also pleased to announce that reduced student conference fees of €400, 
and through our kind sponsors IUCr and MiTeGen, we have early career travel 
grants available. To apply for a grant, please send a letter of recommendation 
from your supervisor to diffmet2...@physnet.uni-hamburg.de 

Confirmed seminar speakers and panel members include:

Marcus Fischer, St. Jude Children's Research Hospital, USA
Karin Khünel, Structure, Germany
Louise Dunnett, Diamond Light Source, UK
Nicholas Pearce, Linköping University, Sweden
Helen Ginn, DESY, Germany

See you in Berlin!
Helena & Ali 

On behalf of the organizers of both events, Graeme Winter, Kunio Hirata, Helena 
Taberman, Ali Ebrahim, Arwen Pearson and Ashwin Chari



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Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Wankowicz, Stephanie]

If it does what it claims – incredibly impressive. The issue we have is there 
is no way to verify or validate the claims it is making.

The letter is a call and start of a conversation about how the ever-changing 
landscape of communication and publication of science should be.

-Stephanie Wankowicz

From: CCP4 bulletin board  on behalf of Krieger, James M 

Sent: Monday, May 13, 2024 10:22 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

It definitely is impressive but it also has clear limitations On 13 May 2024, 
at 15: 22, Sylvia Fanucchi  
wrote:  You don't often get email from d0c4e77ae410-dmarc-request@ 
jiscmail. ac. uk. 
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd
It definitely is impressive but it also has clear limitations

On 13 May 2024, at 15:22, Sylvia Fanucchi 
 wrote:


You don't often get email from d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is 
important
Is it just me who is really impressed by it? Am I missing something?

Get Outlook for 
Android

From: CCP4 bulletin board  on behalf of Rafael Marques 

Sent: Monday, May 13, 2024 3:13:16 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was 
preparing to submit my second job, the first one was already finished, which 
made me think that I was definitely doing something wrong. Probably I was...

Best wishes

Rafael Marques


On 13 May 2024 09:53, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz 
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
>
>
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
> 
>  to disable email stamping for this address.
>
>Hello,
>
>
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work.
>
>
>
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
>
>
>
>Please see the entire letter here. 
> 
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form.
>
>
>
>Additionally, a PDF version of the letter can be found here 
> .
>
>
>
>Thank you,
>
>
>
>Stephanie Wankowicz, UCSF
>
>Pedro Beltrao, ETH
>Benjamin Cravatt, Scripps
>Roland Dunbrack, FCCC
>Anthony Gitter, UW Madison
>Kresten Lindorff-Larsen, Copenhagen
>Sergey Ovchinnikov, MIT
>Nicholas Polizzi, DFCI/HMS
>Brian Shoichet, 

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Krieger, James M]

It definitely is impressive but it also has clear limitations

On 13 May 2024, at 15:22, Sylvia Fanucchi 
 wrote:


You don't often get email from d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is important
Is it just me who is really impressed by it? Am I missing something?

Get Outlook for Android

From: CCP4 bulletin board  on behalf of Rafael Marques 

Sent: Monday, May 13, 2024 3:13:16 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was 
preparing to submit my second job, the first one was already finished, which 
made me think that I was definitely doing something wrong. Probably I was...

Best wishes

Rafael Marques


On 13 May 2024 09:53, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz 
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
>
>
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
>  to disable email stamping 
> for this address.
>
>Hello,
>
>
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work.
>
>
>
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
>
>
>
>Please see the entire letter here. 
> 
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form.
>
>
>
>Additionally, a PDF version of the letter can be found here 
> .
>
>
>
>Thank you,
>
>
>
>Stephanie Wankowicz, UCSF
>
>Pedro Beltrao, ETH
>Benjamin Cravatt, Scripps
>Roland Dunbrack, FCCC
>Anthony Gitter, UW Madison
>Kresten Lindorff-Larsen, Copenhagen
>Sergey Ovchinnikov, MIT
>Nicholas Polizzi, DFCI/HMS
>Brian Shoichet, UCSF
>James Fraser, UCSF
>
>



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Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

[Otsile Mojanaga]

From: Otsile Mojanaga
Sent: Monday, May 13, 2024 3:29 PM
To: Paul Emsley 
Subject: RE: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and 
RX6600XT GPU hardware PC

Dear Paul/All
Thank you for the response. I am on Windows 11 and I tried looking around Coot 
to see where I could input the commands you have suggested but I cannot find 
anything . I also cannot seem to type the commands into the 'Command prompt' 
that opens alongside Coot. I also tried inputting the commands in the 'Coot 
Python scripting' within Coot but this did not work. Please advise on when you 
can input these commands.

Kind regards,
Otsile

From: Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>>
Sent: Monday, May 13, 2024 1:48 PM
To: Otsile Mojanaga mailto:oo...@bath.ac.uk>>; 
CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and 
RX6600XT GPU hardware PC

You don't often get email from 
pems...@mrc-lmb.cam.ac.uk. Learn why this is 
important
CAUTION:  This email came from outside of the University. To keep your account 
safe, only click on links and open attachments if you know the person who sent 
the email, or you expected to receive this communication.




On 13/05/2024 13:03, Otsile Mojanaga wrote:
Dear All
I have been using coot as part of my normal workflow but since last week I have 
been having issues with Coot after I built my own PC which contains the 
following Hardware:
CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads
RAM - 64 GB
GPU - AMD Radeon RX 6600 XT - Primary/Discrete
GPU VRAM - 8176 MB - GDDR6 2000 MHz

Despite the improvement in hardware, Coot is now having issues refining 
molecules when using the 'real space refine' tool and other related tools. When 
trying to refine, the program becomes stuttering and slow such that it becomes 
unfeasible to use the program in a reasonable amount of time. My current work 
around is to run Coot through CCP4 cloud but this greatly slows down my 
workflow. >From what I can see Coot is not be optimised for the AMD CPU.


You don't mention the operating system.

Maybe you have too many threads for Coot? Try setting the COOT_N_THREADS to 
various values (starting, say, with 2) and see what happens.

But maybe it's a graphics (driver) issue and not a CPU/threads issue. glxgears 
is the classic test for that.

Paul.





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Re: [ccp4bb] What could these crystals be?

[Jon Cooper]

Hello, what is in the purification buffer?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 13 May 2024, 15:15, 张慧欣 wrote:

> Hi all
> We have been trying with no success to crystalize a protein. Recently we got 
> these strange shape "crystals". They are hard and flat . Any ideas as to what 
> could cause this? The crystallization conditions is:0.06M Divalents 0.1M 
> BICINE 0.1M Tris pH8.5 20% Ethylene glycol 10% PEG8000
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre

[David Lawson (JIC)]

Hi All,

The John Innes Centre in Norwich (UK) will be hosting this year’s CCP4-BCA 
Protein Crystallography Summer School.

Please follow this link for more details and to apply:
https://www.jic.ac.uk/event/ccp4-bca-protein-crystallography-summer-school-2024/

Best wishes

Dave

---

Prof. David M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk





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[ccp4bb] Scientific Coordinator post - grade 8 Oxford University

[Alex Bullock]

Please forward If you know anyone who might be interested in a drug discovery 
senior scientific coordinator post ...

We are seeking to appoint a Programme Manager/Scientific Coordinator at the 
University of Oxford's Centre for Medicines Discovery (CMD). The CMD was 
established in 2020 with the ambition to help pioneer new treatments for 
disease (https://www.cmd.ox.ac.uk/).
To realise this ambition, the CMD is forming extensive collaborations with 
academics across the University of Oxford and beyond to help translate basic 
science into new drug discovery projects, as well as partnerships with industry 
to develop drug leads into new medicines.

This role presents an exciting opportunity to engage with a large number of 
world-leading academics and clinicians, as well as funders and industry 
representatives on a diverse portfolio of projects. The postholder will help to 
establish strategic alliances for the department, help to write funding 
applications for new projects and contribute to their successful project 
management. You will be expected to supervise an associated project manager and 
will have the support of other Senior Programme Managers and Principal 
Investigators in the department. Successful projects will have a clear research 
and financial path to the clinic.

This position is offered full time on a fixed term contract until 31 March 2026 
(with potential for extension) and is funded by NIHR BRC Oxford and Oxford 
Health.


Job link can be found here - Job Details 
(corehr.com)
Also on linkedin https://www.linkedin.com/jobs/view/3922102066
closing date of 3 June 2024.

Thanks
Alex Bullock
alex.bull...@cmd.ox.ac.uk




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Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Sylvia Fanucchi]

Is it just me who is really impressed by it? Am I missing something?

Get Outlook for Android

From: CCP4 bulletin board  on behalf of Rafael Marques 

Sent: Monday, May 13, 2024 3:13:16 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was 
preparing to submit my second job, the first one was already finished, which 
made me think that I was definitely doing something wrong. Probably I was...

Best wishes

Rafael Marques


On 13 May 2024 09:53, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz 
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
>
>
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
>  to disable email stamping 
> for this address.
>
>Hello,
>
>
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work.
>
>
>
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
>
>
>
>Please see the entire letter here. 
> 
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form.
>
>
>
>Additionally, a PDF version of the letter can be found here 
> .
>
>
>
>Thank you,
>
>
>
>Stephanie Wankowicz, UCSF
>
>Pedro Beltrao, ETH
>Benjamin Cravatt, Scripps
>Roland Dunbrack, FCCC
>Anthony Gitter, UW Madison
>Kresten Lindorff-Larsen, Copenhagen
>Sergey Ovchinnikov, MIT
>Nicholas Polizzi, DFCI/HMS
>Brian Shoichet, UCSF
>James Fraser, UCSF
>
>



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This communication is intended for the addressee only. It is confidential. If 
you have received this communication in error, please notify us immediately and 
destroy the original message. You may not copy or disseminate this 
communication without the permission of the University. Only authorised 
signatories are competent to enter into agreements on behalf of the University 
and recipients are thus advised that the content of this message may not be 
legally binding on the University and may contain the personal views and 
opinions of the author, which are not necessarily the views and opinions of The 
University of the Witwatersrand, Johannesburg. All agreements between the 
University and outsiders are subject to South African Law unless the University 
agrees in writing to the contrary.



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Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Rafael Marques]

I tried it yesterday and I was really shocked by how fast it is. When I was preparing to submit my second job, the first one was already finished, which made me think that I was definitely doing something wrong. Probably I was...Best wishes Rafael Marques On 13 May 2024 09:53, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:Hi folks



This arrived in my inbox this morning, and I believe that it may provoke some discussion…



Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν



Best wishes!



Harry



>    From: Stephanie Wankowicz  

>    Sent: Saturday, May 11, 2024 3:31 PM

>    To: James Fraser ; Pedro Beltrao ; Benjamin Cravatt ; Roland Dunbrack ; Anthony Gitter ; Kresten Lindorff-Larsen ; Sergey Ovchinnikov ; Polizzi, Nicholas F. ; Brian Shoichet 

>    Subject: AlphaFold3 Transparency and Reproducibility

> 

> 

>    This email from mullane.stepha...@gmail.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list  to disable email stamping for this address. 

> 

>    Hello,

> 

> 

>    As many of you, we were incredibly disappointed with the lack of code or even executables accompanying the publication of AlphaFold3 in Nature. AlphaFold3 was released without the means to test and use the software in a high-throughput manner. This does not align with the principles of scientific research, which rely on the ability of the community to evaluate, use, and build upon existing work. 

> 

> 

> 

>    We have written a letter, which will be posted on Zenodo and submitted as a Letter to the Editor in the coming days.

> 

> 

> 

>    Please see the entire letter here.  If you want to endorse this letter, please fill out your name, affiliation, and email in the form. 

> 

> 

> 

>    Additionally, a PDF version of the letter can be found here . 

> 

> 

> 

>    Thank you, 

> 

> 

> 

>    Stephanie Wankowicz, UCSF

> 

>    Pedro Beltrao, ETH

>    Benjamin Cravatt, Scripps

>    Roland Dunbrack, FCCC

>    Anthony Gitter, UW Madison

>    Kresten Lindorff-Larsen, Copenhagen

>    Sergey Ovchinnikov, MIT

>    Nicholas Polizzi, DFCI/HMS

>    Brian Shoichet, UCSF

>    James Fraser, UCSF

> 

> 







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Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

[Paul Emsley]

On 13/05/2024 13:03, Otsile Mojanaga wrote:


Dear All

I have been using coot as part of my normal workflow but since last 
week I have been having issues with Coot after I built my own PC which 
contains the following Hardware:


CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads

RAM - 64 GB

GPU - AMD Radeon RX 6600 XT - Primary/Discrete

GPU VRAM - 8176 MB - GDDR6 2000 MHz

Despite the improvement in hardware, Coot is now having issues 
refining molecules when using the ‘real space refine’ tool and other 
related tools. When trying to refine, the program becomes stuttering 
and slow such that it becomes unfeasible to use the program in a 
reasonable amount of time. My current work around is to run Coot 
through CCP4 cloud but this greatly slows down my workflow. >From what 
I can see Coot is not be optimised for the AMD CPU.



You don't mention the operating system.

Maybe you have too many threads for Coot? Try setting the COOT_N_THREADS 
to various values (starting, say, with 2) and see what happens.


But maybe it's a graphics (driver) issue and not a CPU/threads issue. 
glxgears is the classic test for that.


Paul.




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[ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

[Otsile Mojanaga]

Dear All
I have been using coot as part of my normal workflow but since last week I have 
been having issues with Coot after I built my own PC which contains the 
following Hardware:
CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads
RAM - 64 GB
GPU - AMD Radeon RX 6600 XT - Primary/Discrete
GPU VRAM - 8176 MB - GDDR6 2000 MHz

Despite the improvement in hardware, Coot is now having issues refining 
molecules when using the 'real space refine' tool and other related tools. When 
trying to refine, the program becomes stuttering and slow such that it becomes 
unfeasible to use the program in a reasonable amount of time. My current work 
around is to run Coot through CCP4 cloud but this greatly slows down my 
workflow. From what I can see Coot is not be optimised for the AMD CPU.

Any help or would be greatly appreciated.

Kind regards,
Otsile



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Re: [ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

[Paul Emsley]

On 13/05/2024 11:23, Laurent Maveyraud wrote:

Hello,
I like the function "update NCS ghosts with local match" found in the 
calculate/NCT tools menu. It's really helpful when NCS is not really 
strict. However, I find it clumsy that you have to go in a submenu to 
get it, so I would like to define a keyboard shortcut... this would be 
much faster.


Which function should I use to  do that ?

(add_key_binding "Update ghosts" "a" (unknown function)



(add-key-binding "Update NCS Ghosts" "a" update-ncs-ghosts-by-local-sphere)

P.



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Re: [ccp4bb] Postdoctoral position at the Sussex Drug Discovery Centre

[Erika Mancini]

Dear ccp4bb community,

There are just a few days left to apply for this position - deadline 17th of 
May.
Many thanks


We have a postdoctoral position available to join the Drug Discovery team at 
the Sussex Drug Discovery Centre (SDDC) under the supervision of Prof Erika 
Mancini and Prof John Spencer.
The successful candidate will work in a multidisciplinary environment on an 
exciting and emerging area of oncology drug discovery and interact closely with 
our cellular biology and medicinal chemistry teams.
The Post-doc will be involved in high-throughput X-ray crystallography, 
fragment-based screening and structure-based drug design and will be 
responsible for crystallisation, structure determination, structural and 
biophysical analysis of protein-ligand complexes.
This is a one year contract funded by Omaze-Blood Cancer UK for a collaborative 
project with the group of Prof Nerlov at the University of Oxford.

For more information on the job and how to apply, please visit the following 
link:
https://jobs.sussex.ac.uk/job/91c964e4-e58f-4504-aafe-ca239bf7220b

[https://cdn1.site-media.eu/images/1200x630/6990143/logo-black.png]
Research Fellow Ref 30876 - Job page - University of Sussex Job 
Search
jobs.sussex.ac.uk
For any questions, feel free to send me an email.
Erika




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Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Pedro Matias]

Hi Harry,

Thanks for sharing this. I already read and endorsed the letter.

However, I do have a comment - since one of the letter signatories was a 
reviewer of the paper, wouldn't the shortcomings described in the letter 
be grounds for rejection of the manuscript?


Best regards,

Pedro

On 13/05/2024 09:53, Harry Powell wrote:

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry


From: Stephanie Wankowicz 
Sent: Saturday, May 11, 2024 3:31 PM
To: James Fraser ; Pedro Beltrao ; Benjamin Cravatt 
; Roland Dunbrack ; Anthony Gitter ; 
Kresten Lindorff-Larsen ; Sergey Ovchinnikov ; Polizzi, Nicholas F. 
; Brian Shoichet 
Subject: AlphaFold3 Transparency and Reproducibility


This email from mullane.stepha...@gmail.com originates from outside Imperial. Do 
not click on links and attachments unless you recognise the sender. If you trust the 
sender, add them to your safe senders list 
 to disable email stamping for 
this address.

Hello,


As many of you, we were incredibly disappointed with the lack of code or 
even executables accompanying the publication of AlphaFold3 in Nature. 
AlphaFold3 was released without the means to test and use the software in a 
high-throughput manner. This does not align with the principles of scientific 
research, which rely on the ability of the community to evaluate, use, and 
build upon existing work.



We have written a letter, which will be posted on Zenodo and submitted as a 
Letter to the Editor in the coming days.



Please see the entire letter here. 

 If you want to endorse this letter, please fill out your name, affiliation, and 
email in the form.



Additionally, a PDF version of the letter can be found here 
.



Thank you,



Stephanie Wankowicz, UCSF

Pedro Beltrao, ETH
Benjamin Cravatt, Scripps
Roland Dunbrack, FCCC
Anthony Gitter, UW Madison
Kresten Lindorff-Larsen, Copenhagen
Sergey Ovchinnikov, MIT
Nicholas Polizzi, DFCI/HMS
Brian Shoichet, UCSF
James Fraser, UCSF





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--
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



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[ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

[Laurent Maveyraud]

Hello,
I like the function "update NCS ghosts with local match" found in the 
calculate/NCT tools menu. It's really helpful when NCS is not really 
strict. However, I find it clumsy that you have to go in a submenu to 
get it, so I would like to define a keyboard shortcut... this would be 
much faster.


Which function should I use to  do that ?

(add_key_binding "Update ghosts" "a" (unknown function)

thanks a lot !

Laurent

--
logo-ipbs


 Laurent Maveyraud


   Professor of Biophysics | University of Toulouse

Doctoral School Biology - Health - Biotechnologies

+33 5 61 17 54 35 | +33 6 46 04 21 11 | laurent.maveyr...@ipbs.fr 



UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse 
Cedex 4


ipbs.fr 

@IpbsToulouse 

ipbs.cnrs 

our group  












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[ccp4bb] In-Silico Structural Biology School - Bari, October 2024

[Mazzorana, Marco (DLSLtd,RAL,LSCI)]

Dear CCP4bb’ers,
On behalf of the organizing team and of the Italian Crystallographic 
Association (AIC) teaching committee, I am pleased to announce this year’s AIC 
School, organized in partnership with the GENe to Structure (GENS) team 
(website).

Registrations are now open to “In-Silico Structural Biology”, a 4-day School 
focusing on the exploitation of computational methods for structural biology 
investigations, from molecular docking to artificial intelligence for 
structural biology applications.

The aim of the School is to introduce young researchers from the fields of 
chemistry, structural biology, biophysics, and biochemistry to the latest 
developments in the area, providing theoretical background and practical 
overview of state-of-the-art tools.

The speaker line-up includes:

  *   Dragos Horvath, University of Strasbourg (FR)
  *   Gianluca Lattanzi, University of Trento (IT)
  *   Rocco Caliandro, Consiglio Nazionale delle Ricerche (IT)
  *   Joana Pereira, University of Basel (CH)
  *   Giuseppe Mangiatordi, Consiglio Nazionale delle Ricerche (IT)
  *   Benny Danilo Belviso, Consiglio Nazionale delle Ricerche (IT)
  *   Alessandro Landi, University of Salerno (IT)
  *   Pietro Delre, Consiglio Nazionale delle Ricerche (IT)
  *   Ciro Pierri, University of Bari (IT)

The School will be held in person 28th-31st October 2024 in Bari (Area di 
Ricerca CNR).

For more information, program details, and registration, please visit:
https://www.gene2structure.it/issb/
https://school2024.cristallografia.org/

Registration deadline: 1st July 2024

For any queries about the school, please contact directly 
secretar...@gene2structure.it

Best wishes,

Marco



--
Marco Mazzorana, PhD
MX beamline scientist
DR1-46, Diamond Light Source
Didcot (UK)

Tel: +44 (0)1235 778643
Email: marco.mazzor...@diamond.ac.uk


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 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
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Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

[Thorn, Dr. Andrea]

Renato and Stuart McNicholls wrote exactly the right thing: deleting this file 
resolved the issue. Thank you very much!

-Original Message-
From: CCP4 bulletin board  On Behalf Of Renato Weiße
Sent: 08 May 2024 16:44
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

Hi Andrea,

concerning Log #1: there is a log file 
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml, which is 
probably empty. If it is, then deleting it should resolve the error. I have 
seen this problem from time to time on students laptops, but could not figure 
out, for what reason it occurs.

Cheers,
Renato


Zitat von "Thorn, Dr. Andrea" :

> Dear all,
> My ccp4i2 installation stopped working - it does not start up  
> properly anymore (see Log #1 below for the output).
> I started ccp4i which brought up the update manager and ran  
> outstanding updates. This did not fix the issue. I also sourced the  
> source file manually, just to make sure.
> Then I ran ./find-missing-libs.sh and fixed some issues, but got  
> stuck (see Log #2 below).
> Deleting the ccp4 folder and re-install also did not help.
> The system is Ubuntu in a virtual box.
> I would be grateful for any advice.
> Best wishes,
>
> Andrea.
>
> __
>
> LOG #1:
>
> Running CCP4i2 browser from:  
> /opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2
> Python 3.7.12 (default, Jan  6 2022, 21:30:12)
> [GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
> Qt version 5.15.2
>
> Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use  
> QT_QPA_PLATFORM=wayland to run on Wayland anyway.
> Sandboxing disabled by user.
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.browser.py'
> [0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> [0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> [0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> [0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> ccp4i2 version 1.1.0
> ccp4i2 source revision 6539
> CPrintHandler saving print output to directory:  
> /home/athorn/.CCP4I2/logs/started_1715177113
> None
> None
> Starting Project Manager
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> Starting Project Manager - DONE
> Starting Job Controller
> Starting Job Controller - DONE
> 
> isDarkMode? False
> 
> Starting   0.00048089027404785156
> StyleSheet screen size: 1920 1089
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> CCP4i2 starting HTTP server on 127.0.0.1 port 43434
>
> Retrieving status  
> file:/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml
> Traceback (most recent call last):
>   File  
> "/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py",  
> line 266, in openFileToEtree
> tree = parse_from_unicode(s,useLXML=useLXML)
>   File  
> 

[ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Harry Powell]

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz  
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
> 
> 
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
>  to disable email stamping 
> for this address. 
> 
>Hello,
> 
> 
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work. 
> 
> 
> 
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
> 
> 
> 
>Please see the entire letter here. 
> 
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form. 
> 
> 
> 
>Additionally, a PDF version of the letter can be found here 
> .
>  
> 
> 
> 
>Thank you, 
> 
> 
> 
>Stephanie Wankowicz, UCSF
> 
>Pedro Beltrao, ETH
>Benjamin Cravatt, Scripps
>Roland Dunbrack, FCCC
>Anthony Gitter, UW Madison
>Kresten Lindorff-Larsen, Copenhagen
>Sergey Ovchinnikov, MIT
>Nicholas Polizzi, DFCI/HMS
>Brian Shoichet, UCSF
>James Fraser, UCSF
> 
> 



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[ccp4bb] Post-doctoral position protein-nucleic acid complexes Granneman lab

[Sander Granneman]

I am a group leader at the University of Edinburgh (Granneman 
Lab), Scotland, UK, and I have a 
post-doc position available for a structural biologist.

The post, funded by a Medical Research Council programme grant,  is initially 
for 2 years but can be extended to 4 years.
I am looking for an experienced structural biologist that has a track record in 
structural analysis (X-ray crystallography and/or cryo-EM) of protein complexes.
The project aims to understand how helix-turn-helix proteins in bacteria are 
also able to recognise RNA and what the functional significance of this 
interaction is.
It is a hugely interdisciplinary project, involving biochemistry, biophysics, 
computational analysis of sequencing data and drug discovery and therefore 
provides a unique learning opportunity for scientists willing to expand their 
toolset. We don't expect you to have knowledge in all of these areas! The most 
important thing is that the candidate has experience in structural biology and 
biophysical analysis of protein-ligand interactions.

Feel free to e-mail me (sander.granne...@ed.ac.uk) to discuss this further.

All the best,

Sander

Associate Professor at the University of Edinburgh
Centre for Engineering Biology
The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh 
Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.



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