Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Soisson, Stephen M]

A wonderful idea Gerard and Clemens.

Sent from my iPhone

> On Mar 18, 2020, at 6:31 PM, Gerard Bricogne  wrote:
> 
> EXTERNAL EMAIL – Use caution with any links or file attachments.
> 
> Dear colleagues,
> 
> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> structures in the PDB seems to indicate that that there might be potential
> to improve these if refinements could be repeated after some reprocessing
> and further analysis of the raw diffraction images, rather than against the
> deposited merged data. This statement should in no way be construed as a
> criticism of the remarkable achievements of the research groups concerned,
> who have been operating under tremendous time pressure, but as an exciting
> opportunity to push methods to their limits on a uniquely significant class
> of structures.
> 
> Another consideration is that the various logistical problems created by
> COVID-19 may soon make it increasingly difficult to collect new diffraction
> data on potential drug targets relevant to the fight against SARS-CoV-2,
> underlining the importance of ensuring that the best results be obtained
> from every dataset actually collected, and that the most useful conclusions
> be drawn from the analysis of those datasets towards improving the quality
> of subsequent data collections. 
> 
> On this basis we would like to propose that special efforts be made to grant
> public access to the raw image data associated with any SARS-CoV-2 related
> structure that is deposited into the PDB. This can be done by (1) archiving
> these raw image data using resources such as data.sbgrid.org, zenodo.org,
> proteindiffraction.org or any other cloud-based data-sharing service, and
> (2) communicating the corresponding DOIs to the wwPDB centres. This idea
> could be extended to datasets that investigators would like to offer to
> interested methods developers or expert users at the pre-deposition stage.
> 
> Experts making use of those raw data would be encouraged to document, in as
> much detail as possible, how particular programs or workflows could be used
> on those structures/datasets to obtain the best results. This would be a
> kind of "virtual workshop", a particularly valuable collective activity at
> the present time when several in-person workshops (e.g. RapiData) have been
> cancelled and many meetings are in limbo for several months.
> 
> The latter activity would benefit from having a centralised facility set up
> for the experts to post their results and annotations: we could create such
> a facility, but other, larger groups might want to consider doing so. 
> 
> 
> With best wishes,
> 
> Clemens & Gerard.
> 
> 
> 
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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Diana Tomchick]

​Frankly this is a great idea for datasets on any projects. I've been so busy 
the last 3-4 years that I have been unable to do it for my projects, but now I 
should be able to get it done. Not to mention trying to solve a couple of those 
pesky structures that have proven tough nuts to crack.


Diana


**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, March 18, 2020 5:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

EXTERNAL MAIL

What a great idea? Have you approached the depositors? Eleanor

On Wed, 18 Mar 2020 at 22:31, Gerard Bricogne 
mailto:g...@globalphasing.com>> wrote:
Dear colleagues,

Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than against the
deposited merged data. This statement should in no way be construed as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.

Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections.

On this basis we would like to propose that special efforts be made to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as 
data.sbgrid.org, zenodo.org,
proteindiffraction.org or any other cloud-based 
data-sharing service, and
(2) communicating the corresponding DOIs to the wwPDB centres. This idea
could be extended to datasets that investigators would like to offer to
interested methods developers or expert users at the pre-deposition stage.

Experts making use of those raw data would be encouraged to document, in as
much detail as possible, how particular programs or workflows could be used
on those structures/datasets to obtain the best results. This would be a
kind of "virtual workshop", a particularly valuable collective activity at
the present time when several in-person workshops (e.g. RapiData) have been
cancelled and many meetings are in limbo for several months.

The latter activity would benefit from having a centralised facility set up
for the experts to post their results and annotations: we could create such
a facility, but other, larger groups might want to consider doing so.


With best wishes,

Clemens & Gerard.



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Eleanor Dodson]

What a great idea? Have you approached the depositors? Eleanor

On Wed, 18 Mar 2020 at 22:31, Gerard Bricogne 
wrote:

> Dear colleagues,
>
> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> structures in the PDB seems to indicate that that there might be potential
> to improve these if refinements could be repeated after some reprocessing
> and further analysis of the raw diffraction images, rather than against the
> deposited merged data. This statement should in no way be construed as a
> criticism of the remarkable achievements of the research groups concerned,
> who have been operating under tremendous time pressure, but as an exciting
> opportunity to push methods to their limits on a uniquely significant class
> of structures.
>
> Another consideration is that the various logistical problems created by
> COVID-19 may soon make it increasingly difficult to collect new diffraction
> data on potential drug targets relevant to the fight against SARS-CoV-2,
> underlining the importance of ensuring that the best results be obtained
> from every dataset actually collected, and that the most useful conclusions
> be drawn from the analysis of those datasets towards improving the quality
> of subsequent data collections.
>
> On this basis we would like to propose that special efforts be made to
> grant
> public access to the raw image data associated with any SARS-CoV-2 related
> structure that is deposited into the PDB. This can be done by (1) archiving
> these raw image data using resources such as data.sbgrid.org, zenodo.org,
> proteindiffraction.org or any other cloud-based data-sharing service, and
> (2) communicating the corresponding DOIs to the wwPDB centres. This idea
> could be extended to datasets that investigators would like to offer to
> interested methods developers or expert users at the pre-deposition stage.
>
> Experts making use of those raw data would be encouraged to document, in as
> much detail as possible, how particular programs or workflows could be used
> on those structures/datasets to obtain the best results. This would be a
> kind of "virtual workshop", a particularly valuable collective activity at
> the present time when several in-person workshops (e.g. RapiData) have been
> cancelled and many meetings are in limbo for several months.
>
> The latter activity would benefit from having a centralised facility set up
> for the experts to post their results and annotations: we could create such
> a facility, but other, larger groups might want to consider doing so.
>
>
> With best wishes,
>
> Clemens & Gerard.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Gerard Bricogne]

Dear colleagues,

Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than against the
deposited merged data. This statement should in no way be construed as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.

Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections. 

On this basis we would like to propose that special efforts be made to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as data.sbgrid.org, zenodo.org,
proteindiffraction.org or any other cloud-based data-sharing service, and
(2) communicating the corresponding DOIs to the wwPDB centres. This idea
could be extended to datasets that investigators would like to offer to
interested methods developers or expert users at the pre-deposition stage.

Experts making use of those raw data would be encouraged to document, in as
much detail as possible, how particular programs or workflows could be used
on those structures/datasets to obtain the best results. This would be a
kind of "virtual workshop", a particularly valuable collective activity at
the present time when several in-person workshops (e.g. RapiData) have been
cancelled and many meetings are in limbo for several months.

The latter activity would benefit from having a centralised facility set up
for the experts to post their results and annotations: we could create such
a facility, but other, larger groups might want to consider doing so. 


With best wishes,

Clemens & Gerard.



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[ccp4bb] Postdoc position, Sugar Transporting Membrane Proteins (Denmark), [repost]

[Bjørn Panyella Pedersen]

Dear colleagues,
Please pass this along any one who might be interested. Thanks!
/Bjørn


Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at 
Aarhus University, Denmark.

online posting:
http://tiny.cc/MBG_postdoc

We are looking for a highly skilled and motivated postdoc with an interest in 
working on sugar transporting membrane transporters and preferably with a 
proven track record in the area of structural and/or functional analysis of 
membrane proteins.

The position will be open from summer 2020, but starting date is negotiable. 
Funding is available for at least 2 years of employment, with an automatic 
extension possible for up to a total maximum of 4 years.

The position:
The position seeks to strengthen ongoing activities in the laboratory of Bjørn 
P. Pedersen on structure, related to the function and mechanism of 
sugar-transporting membrane proteins (pedersenlab.dk). The laboratory's 
interest is the interplay between structure and function of transmembrane 
transport processes with a focus on metabolite uptake systems, and the methods 
uses are primarily crystallography, cryo-EM and biochemistry. The group is part 
of the Section of Structural Biology at Aarhus University.

The candidate:
A successful candidate has a relevant Ph.D. degree and a solid and documented 
background in structural biology, biochemistry and/or biophysics. Experience 
with membrane protein expression and purification is favored, and the candidate 
must demonstrate an ability and interest to work with membrane proteins with a 
structural aim. Applicants should be ambitious, show strong collaborative 
skills, and be able to take initiatives and responsibility within the work 
environment.

The successful candidate is offered:
- access to a well-developed research infrastructure.
- a research climate inviting lively, open and critical discussion within and 
across different fields of research.
- a working environment with teamwork, close working relations, network 
activities among young scientists and social activities.
- a workplace characterized by professionalism, equality and a healthy 
work-life balance.

The city:
In Aarhus you have easy access to beautiful nature, an exciting culture and 
city life as well as a safe environment for children - a great place for the 
whole family. The city of Aarhus has everything you need: exciting national and 
international jobs, delightful residential areas, a rich cultural life, and 
beautiful surrounding landscape of woods and coastline that make Aarhus a 
wonderful place to live and work.

Deadline:
All applications must be made online (http://tiny.cc/MBG_postdoc) and received 
by 2. apr. 2020.





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[ccp4bb] NCCAT 2020 CryoEM Short course in SPA now online - NYC, USA

[Ed Eng]

Dear all,


The NCCAT Single-Particle Analysis short course that was held March 2-6 is now 
available for viewing on YouTube on the NRAMM SEMC NCCAT channel:  
https://www.youtube.com/playlist?list=PLhiuGaXlZZel2mj6S4FPjWwsvj2LPqLYL .


The agenda and PDF of the slides that were presented can be found on the 
workshop website:

https://nccat.nysbc.org/activities/courses/nccat-spa-short-course-2020/ .


Stay tuned for more online remote content that we will be releasing over the 
next few weeks. Any interested students are welcome to request to attend remote 
video conference office hours to follow up on the SPA short course material and 
additional cryoEM cross-training curricula. If you are interested in signing up 
for updates and more information please go to: 
https://www.surveymonkey.com/r/NCCAT-remote  .


Best,

Ed Eng

National Center for CryoEM Access and Training (NCCAT)

New York Structural Biology Center



The Transformative High Resolution Cryo-Electron Microscopy Program

commonfund.nih.gov/CryoEM




---
Edward T. Eng, Ph.D.
NCCAT: National Center for CryoEM Access and Training
SEMC: Simons Electron Microscopy Center
NYSBC: New York Structural Biology Center
89 Convent Ave, NY, NY 10027
nccat.nysbc.org semc.nysbc.org
(212)939-0660 x346



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