Re: [ccp4bb] Is this Spam? This looks like Spam.

[Goldman, Adrian]

Me too. My uni says that a Microsoft set of addresses ended up on a spam 
blacklist, which is why this happened. I suspect your institutions are also 
using office365 outlook (also known as crapmail) as mail server and client

As roberto, I complain all the time to my uni about their mail and it. Probably 
as roberto, it has no effect whatsoever.

Adrian

Sent from my iPhone

On 11 Jan 2023, at 23:13, Becker, Stefan  wrote:

 I also received this kind of message. Is it definitely spam? I waited for 24 
hours and noticed that no messages appeared under CCP4BB. Then I re-registered 
with CCP4BB. From that moment I received messages again.

Best,
Stefan Becker



Am 10.01.2023 um 15:23 schrieb Bernhard Rupp 
mailto:hofkristall...@gmail.com>>:

I got unsubscribed from ccp4em yesterday with a similar message for 
b...@ruppweb.org. That one has a minor certificate 
problem that however does not affect other email recepients.

For some reason, the ssl certificate for https://ruppweb.org/ is valid, but the 
mailserver still seems to have an issue. May be your IT can check yours

Best br


On Tue, Jan 10, 2023, 02:57 David Briggs 
mailto:david.bri...@crick.ac.uk>> wrote:
I received this odd-looking message from the board address. Did anyone else get 
anything similar?
[cid:b20d59ac-fc29-4cbb-b7f0-65ef44f06b97]
I'm sharing a screenshot because I'm not:
(a) going to click those links
(b) get others to click those links.

Can the board admin confirm if this is legitimate or not?

D

--
Dr David C. Briggs CSci MRSB
Principal Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs

The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Future Diffraction Methods

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear All,

This was not really discussed widely at the study weekend however I think we 
have a core group of people who are sufficiently committed to the “GRC on 
diffraction methods” cause that we will keep it alive - as chair elect I also 
hold a very strong belief that we should keep this going.

Currently we are exploring the opportunities for the “not the GRC on 
diffraction methods 2024” with an intent on keeping the spirit of the meeting 
alive, ideally with the meeting at about the same time it would have happened 
if the GRC had not been cancelled.

Best wishes Graeme


On 5 Jan 2023, at 14:04, Dekker, Carien 
mailto:carien.dek...@novartis.com>> wrote:

Happy New Year all,

Since I am not at the CCP4 weekend (which is happening right now), I would be 
curious to hear if this is/was discussed and what people think.

Carien

-Original Message-
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Frank von Delft
Sent: Monday, December 19, 2022 10:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Future Diffraction Methods

This Message is from an External Sender. Do not click links or open attachments 
unless you trust the sender.

Shoot... that sucks.

Yes, we do need something!

"Structural Biology Methods"?


More interesting question:  does it need the GRC to host?  What about 
reimagining the CCP4 study weekend - the question keeps coming up there anyway.

That's one for CCP4 WG1 to discuss - they're meeting straight after New Year, 
so maybe James, you and Ivo should hop on a zoom and kick the idea around.

Frank



On 16/12/2022 22:10, James Holton wrote:
I want to thank everyone who attended the 2022 Gordon Research
Conference and Gordon Research Seminar on Diffraction Methods in
Structural Biology, as well as all those who contributed to these
great gatherings in the past.  It was an outstanding meeting if I do
say so myself. Not just because it had been so long without in-person
interaction, not just because we had zero covid cases (which I see as
no small feat of Mind over Virus), but because of this amazing
community. It is rare in this world to have such a strong spirit of
collaboration, camaraderie and openness in undertakings as high-impact
as this. Surmounting the barriers to atomic-detail imaging of
biological systems has never been more exciting and more relevant.  I
am proud to be a part of it, and honored to have served as Chair.

It is therefore with heavy heart that I report to this community that
I was the last Chair of the Diffraction Methods GRC.

The GRC Conference Evaluation Committee
(https://urldefense.com/v3/__https://www.grc.org/about/conference-eval
uation-committee/__;!!N3hqHg43uw!seKRCwqf-9U5a5vpm19quTE94sOBoM1HzktB2
NDBxOp6TFV8LC_s19p5TJcgvxfLfp8BheaUlg1wOfursEBNL8h62_DMr_f2M1U$ )
voted this year to discontinue the Diffraction Methods GRC and GRS.
This ends a 46-year tradition that I feel played a vital, and vibrant
role in the work of the people who answer questions on this BB. The
reason given was insufficient attendance.  All other metrics, such as
evaluation surveys and demographics were very strong. I have tried to
appeal, but I'm told the vote was unanimous and final. I understand
that like so many conference organizing bodies the GRC is having to make tough 
financial decisions. I must say I disagree with this one, but it was not my 
decision to make.

Many of the past and elected Chairs have been gathering and discussing
how to replace the Diffraction Methods GRC/GRS going forward. Many
great ideas, advice and perspectives have been provided, but that is a
select group. I feel it is now time to open up this discussion to the
broader community of structural methods developers and practitioners.
There are some important questions to ask:

* How do we define this community?
   Yes, many of us do cryoEM too, but is that one methods
meeting? or two?
* Does this community need a new diffraction methods meeting?
   As in one meeting or zero?
* Should we merge with an existing meeting?
   It would make logistics easier, but a typical GRC has 22 hours
of in-depth presentations over 5 days.  The GRS is 7 hours over 2
days. As Chair, I found that was not nearly enough.
* Where do you think structural methods are going?
   I think I know, but I may be biased.
* Should the name change?
   From 1976 to 2000, it was "Diffraction Methods in Molecular
Biology". The word "diffraction", BTW, comes from the Latin for
"shattering of rays", and originally used to describe the iridescence
of bird feathers. That's spectroscopy!
How about:
"Structural Methods for the Departing of Rays"

I'm sure there are many more questions, and better suggestions.  I
look forward to enlightening discussions!  GRCs have always been about
discussion, and I hope to keep that tradition alive in this community.

-James Holton
MAD Scientist

##
##

To 

Re: [ccp4bb] Is this Spam? This looks like Spam.

[Roberto Steiner]

I got unsubscribed from both ccp4bb and ccpem. I also thought it was spam but 
then realised that I was not getting any message. Complained a bit with our IT 
people (which is something I tend to do anyway) then subscribed again. Since 
then received a bunch of email starting with


> SUBSCRIBE ccp4bb Roberto Steiner
You are already subscribed to the CCP4BB list as "Roberto Steiner".

> Roberto A Steiner
Unknown command - "ROBERTO". Try HELP.


…

but I am now getting ccp4bb emails.

Best wishes
Roberto


Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

Responses to emails are not expected outside of your normal working hours.








On 11 Jan 2023, at 10:15, Becker, Stefan 
mailto:s...@mpinat.mpg.de>> wrote:

You don't often get email from s...@mpinat.mpg.de. 
Learn why this is important
I also received this kind of message. Is it definitely spam? I waited for 24 
hours and noticed that no messages appeared under CCP4BB. Then I re-registered 
with CCP4BB. From that moment I received messages again.

Best,
Stefan Becker



Am 10.01.2023 um 15:23 schrieb Bernhard Rupp 
mailto:hofkristall...@gmail.com>>:

I got unsubscribed from ccp4em yesterday with a similar message for 
b...@ruppweb.org. That one has a minor certificate 
problem that however does not affect other email recepients.

For some reason, the ssl certificate for 
https://ruppweb.org/
 is valid, but the mailserver still seems to have an issue. May be your IT can 
check yours

Best br


On Tue, Jan 10, 2023, 02:57 David Briggs 
mailto:david.bri...@crick.ac.uk>> wrote:
I received this odd-looking message from the board address. Did anyone else get 
anything similar?
[cid:b20d59ac-fc29-4cbb-b7f0-65ef44f06b97]
I'm sharing a screenshot because I'm not:
(a) going to click those links
(b) get others to click those links.

Can the board admin confirm if this is legitimate or not?

D

--
Dr David C. Briggs CSci MRSB
Principal Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs

The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT



To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Jiscmail message on disruption

[Charles Ballard - STFC UKRI]

https://www.jiscmail.ac.uk/20230111-ServiceDisruption.html

"On Thursday, 05 January 2023, we received notification that one of the email 
servers used by JiscMail was listed on a global spam "blacklist", causing 
recipient mail servers to start rejecting JiscMail posts.

We reported the issue to the operators of that email server, and worked with 
them to ensure that the server was removed from the list. By 09:00hrs on Friday 
(06 January) it was confirmed that the server had been removed from the 
blacklist, and that normal service had resumed.

Unfortunately, later that day, the server was re-added to the blacklist, 
causing recipient servers to start rejecting messages once more.

Due to the way in which the software underpinning the JiscMail service works, 
after several bounced or rejected messages to an individual email address, the 
software assumes that the address no longer exists and removes it from any 
subscribed groups. This had the effect of removing around 50,000 subscriptions 
to just short of 500 JiscMail lists.

We are pleased to inform you that, as of 14:00hrs on Wednesday, 11 January 
2023, we believe the root cause of the issue (the blacklisting) to have been 
resolved, and are in the process of resubscribing all affected users. We expect 
this to be completed by no later than 17:00hrs on Wednesday, 11 January 2023.

Despite these issues having been addressed, subscribers and list owners may 
continue to recieve error messages that have been "queued" by mail servers 
outside of our direct control. These are expected to have fully cleared by 
Friday, 13 January 2023.



This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




To unsubscribe from the CCP4BB list, click the following link:
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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Is this Spam? This looks like Spam.

[Becker, Stefan]

I also received this kind of message. Is it definitely spam? I waited for 24 
hours and noticed that no messages appeared under CCP4BB. Then I re-registered 
with CCP4BB. From that moment I received messages again.

Best,
Stefan Becker



Am 10.01.2023 um 15:23 schrieb Bernhard Rupp 
mailto:hofkristall...@gmail.com>>:

I got unsubscribed from ccp4em yesterday with a similar message for 
b...@ruppweb.org. That one has a minor certificate 
problem that however does not affect other email recepients.

For some reason, the ssl certificate for https://ruppweb.org/ is valid, but the 
mailserver still seems to have an issue. May be your IT can check yours

Best br


On Tue, Jan 10, 2023, 02:57 David Briggs 
mailto:david.bri...@crick.ac.uk>> wrote:
I received this odd-looking message from the board address. Did anyone else get 
anything similar?
[cid:b20d59ac-fc29-4cbb-b7f0-65ef44f06b97]
I'm sharing a screenshot because I'm not:
(a) going to click those links
(b) get others to click those links.

Can the board admin confirm if this is legitimate or not?

D

--
Dr David C. Briggs CSci MRSB
Principal Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs

The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT



To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] PDB Reaches a New Milestone: 200,000+ Entries

[Deborah Harrus]

Dear all,

With this week's update, the PDB archive contains a record 200,069 
entries. The archive passed 150,000 structures in 2019 and 100,000 
structures in 2014.


Established in 1971, this central, public archive has reached this 
critical milestone thanks to the efforts of structural biologists 
throughout the world who contribute their experimentally-determined 
protein and nucleic acid structure data.


wwPDB data centers support online access to three-dimensional structures 
of biological macromolecules that help researchers understand many 
facets of biomedicine, agriculture, and ecology, from protein synthesis 
to health and disease to biological energy. Many milestones have been 
reached since the archive released the 100,000th structure in 2014. PDB 
data have been seminal in understanding SARS-CoV-2, and provided the 
foundation for the development of AI/ML techniques for predicting 
protein structure. The 50th anniversary of the PDB was celebrated 
throughout 2021.


Today, the archive is quite large, containing more than 3,000,000 files 
related to these PDB entries that require more than 1086 Gbytes of 
storage. PDB structures contain more than 1.8 billion non-hydrogen atoms.


In the 1950s, scientists had their first direct look at the structures 
of proteins and DNA at the atomic level. Determination of these early 
three-dimensional structures by X-ray crystallography ushered in a new 
era in biology-one driven by the intimate link between form and 
biological function. As the value of archiving and sharing these data 
were quickly recognized by the scientific community, the Protein Data 
Bank (PDB) was established as the first open access digital resource in 
all of biology by an international collaboration in 1971 with data 
centers located in the US and the UK.


Among the first structures deposited in the PDB were those of myoglobin 
and hemoglobin, two oxygen-binding molecules whose structures were 
elucidated by Chemistry Nobel Laureates John Kendrew and Max Perutz. 
With this week's regular update, the PDB welcomes 266 new structures 
into the archive. These structures join others vital to drug discovery, 
bioinformatics and education.


The PDB is growing rapidly, increasing in size ~13% since 2011. In 2022, 
an average of 275 new structures were released to the scientific 
community each week. The resource is accessed hundreds of millions of 
times annually by researchers, students, and educators intent on 
exploring how different proteins are related to one another, to clarify 
fundamental biological mechanisms and discover new medicines.


Since its inception, the PDB has been a community-driven enterprise, 
evolving into a mission critical international resource for biological 
research. The wwPDB partnership was established in July 2003 with PDBe, 
PDBj, and RCSB PDB. Today, the collaboration includes partners BMRB 
(joined in 2006) and EMDB (2021).


The wwPDB ensures that these valuable PDB data are securely stored, 
expertly managed, and made freely available for the benefit of 
scientists and educators around the globe. wwPDB data centers work 
closely with community experts to define deposition and annotation 
policies, resolve data representation issues, and implement community 
validation standards. In addition, the wwPDB works to raise the profile 
of structural biology with increasingly broad audiences.


Each structure submitted to the archive is carefully curated by wwPDB 
staff before release. New depositions are checked and enhanced with 
value-added annotations and linked with other important biological data 
to ensure that PDB structures are discoverable and interpretable by 
users with a wide range of backgrounds and interests.


wwPDB eagerly awaits the next 100,000 structures and the invaluable 
knowledge these new data will bring.


Read more: 
https://www.wwpdb.org/news/news?year=2023#639b9e337f8444f313d20414


Kind regards,

Deborah Harrus

--
---
Deborah Harrus, Ph.D.
Lead Annotator
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] Who will captain the good ship EMDB?

[Gerard Kleywegt]

Dear colleagues,

We are living through unprecedented, exciting times for the cryo-EM field. For 
EMDB, the past decade has been challenging with sustained exponential(!) growth 
of the archive, and rapid methodological changes in the field that need to be 
supported (deposition requirements, metadata, validation).


With continuing major advances in the field (such as in-situ structural 
biology) and progress in other relevant fields (such as accurate 
protein-structure prediction methods), the years ahead promise to be equally 
exciting and challenging for EMDB.


To steer EMDB through the high seas of science, we are looking to recruit a new 
captain, er, Team Leader (an EMBL Faculty position). Are you (or do you know 
someone who is) an ambitious, mid-career scientist who has the skills, drive 
and vision to manage this journey, with the help of an enthusiastic team of 
scientists and software developers?


If you are (or you do), please set sail to: 
https://www.embl.org/jobs/position/EBI02047 for more information.


---

The Electron Microscopy Data Bank (EMDB; emdb-empiar.org) is one of the three 
core archives of the Worldwide Protein Data Bank organisation (wwPDB; 
wwpdb.org). The activities of the EMDB team at EMBL-EBI include archival, 
curation, integration, visualisation, validation and dissemination of cryo-EM 
data, weekly production processes, planning, coordinating and working with our 
wwPDB partners, and outreach, training and public engagement.


We expect the successful candidate to have ample experience with, and a good 
practical and theoretical understanding of cryo-EM/ET, to have experience 
carrying out scientific software development, as well as an ability to write 
successful grants, to manage projects, and to lead a highly skilled team.


The vacancy will close on 23 February 2023 and (virtual) interviews will take 
place on Monday 13 March 2023.


Please feel free to bring this position to the attention of anyone with the 
right skillset who might be interested.


Best wishes,

Gerard Kleywegt & Ardan Patwardhan

---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and  Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Roisin Dunloppdbe_ad...@ebi.ac.uk



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[ccp4bb] Continued issues with CCP4BB

[David Waterman]

Hi folks,

We are continuing to experience some issues with the BB. Jiscmail are aware
of the problems earlier that led to automatic deletion of ~1400 subscribers
and we hope they will reinstate those subscriptions soon. In the meantime,
there appear to be some odd effects like "Rejected posting to
CCP4BB@JISCMAIL.AC.UK" messages being received, even though the messages
have been distributed to the list. If you are unsure, you can always check
the public archive to see if your message has been sent, here:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCP4BB

Jiscmail's service update is on their webpage: https://www.jiscmail.ac.uk/.
Please bear with us for the time being while they resolve the current
issues.

Best wishes,

-- David



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[ccp4bb] Postdoctoral Position in Structural Biology of Pol I and Pol III Transcription, EMBL Heidelberg

[Christoph Mueller]

Dear Colleagues,

The Müller group at EMBL Heidelberg is seeking a highly motivated 
postdoctoral researcher to pursue a cutting-edge experimental research 
project in the structure-function analysis of Pol I and Pol III 
transcription complexes. Depending on the interests of the applicant, 
possible projects will focus on biochemical characterization and 
structure determination by single-particle cryo-EM i/n vitro/ or on 
imaging by cryo-ET, fluorescence microscopy and correlative approaches 
/in situ/.


Further details on the research group can be found at 
https://www.embl.org/groups/mueller/


Applicants should have a PhD in structural molecular biology and 
experience in cryo-EM (single-particle or cryo-ET). To apply and read 
further details on the job description: 
https://www.embl.org/jobs/position/HD02330


Best wishes,
Christoph

__
Dr. Christoph W. Müller
Head of Structural and Computational Biology Unit

EMBL
Meyerhofstrasse 1
69117 Heidelberg, Germany

email:cmuel...@embl.de,christoph.muel...@embl.org
phone: 0049-6221-387-8320
https://www.embl.org
https://www.embl.org/groups/mueller/
___




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[ccp4bb] subscribe

[Delarbre, Laure /FR]

*
Laure Delarbre  < laure.delar...@sanofi.com >

Phone   +33 1 58 93 30 89

BioStructure & Biophysique
Bâtiment Friedel
Sanofi R
13 Quai Jules Guesde
94 400 Vitry sur Seine
France




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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] Is this Spam? This looks like Spam.

[David Waterman]

It looks like there were about 1400 automatic deletions like this across
the CCP4BB. Jisc are aware of the issue, which affects multiple lists (see
https://twitter.com/jiscmailhelp/status/1612756687919742979). We have
requested that these deletions be reverted, but we have not yet heard if
this will be done for us by Jisc or if those subscribers should
re-subscribe themselves. Of course, deleted subscribers will not see this
message...

Cheers

-- David


On Tue, 10 Jan 2023 at 23:11, Bernhard Rupp 
wrote:

> I got unsubscribed from ccp4em yesterday with a similar message for
> b...@ruppweb.org. That one has a minor certificate problem that however
> does not affect other email recepients.
>
> For some reason, the ssl certificate for https://ruppweb.org/ is valid,
> but the mailserver still seems to have an issue. May be your IT can check
> yours
>
> Best br
>
>
> On Tue, Jan 10, 2023, 02:57 David Briggs  wrote:
>
>> I received this odd-looking message from the board address. Did anyone
>> else get anything similar?
>>
>> I'm sharing a screenshot because I'm not:
>> (a) going to click those links
>> (b) get others to click those links.
>>
>> Can the board admin confirm if this is legitimate or not?
>>
>> D
>>
>> --
>>
>> *Dr David C. Briggs CSci MRSB*
>>
>> Principal Laboratory Research Scientist
>>
>> Signalling and Structural Biology Lab
>>
>> The Francis Crick Institute
>>
>> London, UK
>>
>> ==
>>
>> about.me/david_briggs
>>
>> The Francis Crick Institute Limited is a registered charity in England
>> and Wales no. 1140062 and a company registered in England and Wales no.
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[ccp4bb] Postdoctoral position at the Protein Structure Prediction Center, UC Davis

[Andriy Kryshtafovych]

A one-year position focused on large scale analysis of model accuracy 
with respect to applications in structural biology and biology in general.
The UC Davis Protein Structure Prediction Center provides the 
infrastructure to the Critical Assessment of protein Structure 
Prediction program (CASP), dedicated to cutting-edge science in modeling 
of protein structure. It brings together approximately 100 research 
groups from more than 20 countries world-wide.

Desirable skills:
1. In depth knowledge of protein structure
2. Fluency in programming (Perl, PostgreSQL, Python, R and C)
3. Familiarity with Linux
4. Ability to write and run scripts processing data
5. Basic knowledge of computer system administration, including 
multi-processor clusters
6. Knowledge of cgi scripting, web design, and online data visualization 
tools is also desirable


The position is available immediately. With inquiries, please contact 
Krzysztof Fidelis (kfide...@ucdavis.edu).




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