Re: [ccp4bb] Future Diffraction Methods

[Orville, Allen (DLSLtd,RAL,LSCI)]

Hi,

Thanks James, for organising our last GRC meeting.

In the past few years, I’ve also attended one or more Annual BioXFEL 
International Conferences (open, but ending?) and Ringberg Workshop on Science 
with FELs (by invitation only). Both were excellent meetings held in the 
winter, complemented the GRC in diffraction methods, and benefited from 
relatively small attendance with very focused discussions.  I will also add 
that dynamic structural biology is a rapidly growing area that can include 
simultaneous functional, spectroscopic, and structural data collection from the 
same samples, and using synchrotron, XFEL, and/or electron sources. Moreover, 
many of the other life-science centric GRC’s also include significant 
structural data in their frontier programs and discussions (e.g. metals in 
biology, hemes and tetrapyrroles, enzymes, etc.). We are fundamental to 
biochemistry R&D… a broad community indeed.

AMO
~ ~ ~ ~ ~
Allen M. Orville, Ph.D.
Wellcome Investigator and Royal Society Wolfson Fellow
Principal Scientist, XFEL Hub at Diamond Light Source
Harwell Science and Innovation Campus
Didcot, Oxfordshire
OX11 0DE
United Kingdom

Phone: +44 (0) 1235 567505
Mobile: +44 (0) 7471 026061
email: allen.orvi...@diamond.ac.uk

AMO site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub/Staff/Orville.html
XFEL-Hub site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub.html





From: CCP4 bulletin board  on behalf of Frank von Delft 

Date: Monday, 19 December 2022 at 09:22
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Future Diffraction Methods
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://www.grc.org/about/conference-evaluation-committee/) 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"
>

[ccp4bb] Ligand Expo: Scheduled downtime and request for feedback

[Jasmine Young]

Dear CCP4 users,

Ligand Expo (http://ligand-expo.rcsb.org) will be down during the month 
of January 2023. Requests to this service will return a 410 http error 
code (“Gone”) and a message to contact RCSB PDB with any questions.


Users can access CCD data in mmCIF format at 
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/ hashed with the last 
character position, e.g.,


https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/TRP/ 




--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Explore Multiple Sequence Alignments in 1D and 3D at RCSB.org

[Joan Segura]

Dear all,

RCSP PDB is delighted to announce the new 1D-3D Alignment Viewer. The
viewer supports exploration of multiple sequence alignments (MSA) at
sequence and structure levels for PDB experimental structures and Computed
Structure Models (CSMs). Select proteins and/or residue regions from the
MSA to view their 3D structures aligned in Mol*. And options to display (or
hide) other polymeric chains or ligands.

Clusters of protein entity sequences (PDB experimental structures and CSMs)
are calculated by sequence identity threshold or UniProt accession
grouping. For each cluster, its MSA is computed using Clustal Omega
 and displayed in the 1D-3D Alignment Viewer
using specific color schemes. PDB protein sequence positions are
represented in blue if residue was experimentally determined and gray if
not. CSMs are colored according to their local pLDDT scores.



To access this feature, click the 1D-3D Alignments link from any Group
Summary or Group Sequence page (for an example, see the UniProt Group
Summary for O95786
 or Sequence
Identity 241_30
). Group
pages are available from Structure Summary pages (in the Entity Groups
table) and Search Results (more documentation
).


Some examples:

Iron hydrogenase 1


GTPase HRas 

Voltage-dependent calcium channel subunit alpha


Please, send any questions, concerns, or constructive feedback!

Have a tremendous Christmas!!!



-- 
Joan Segura Mora, Ph.D.
Scientific Software Developer
RCSB Protein Data Bank
UCSD, San Diego Supercomputer Center
10100 Hopkins Drive, La Jolla, CA 92093-0505
E-mail: joan.seg...@rcsb.org,
Tel: +1-858-246-0526



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] SERp server alternatives

[Irwin Selvam]

Hi all,

The SERp server appears to be down (https://services.mbi.ucla.edu/SER/). Does 
anyone know of any alternatives or a perhaps a way to run something similar 
locally?

Thanks,

Irwin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Postdoctoral Fellow position in Membrane Protein Biochemistry and CryoEM

[Ankita Punetha]

On behalf of Petrou Lab
-

Dear Colleagues,

A postdoctoral position is available in the Petrou lab at Rutgers New
Jersey Medical School in Newark, New Jersey, to study the structure and
function of membrane (and soluble) proteins using single-particle cryoEM
and other techniques. The Postdoctoral Fellow will be responsible for the
expression, purification and structure determination of proteins involved
in antibiotic resistance or human physiology and pathology. In addition,
the Postdoctoral Fellow will be responsible for biophysical and biochemical
characterization of target proteins, which may include characterization of
protein-ligand or protein-protein interactions.

Candidates must have a Ph.D. in Structural Biology, Molecular Biology,
Biochemistry, or related fields. Preference will be given to candidates
with experience in membrane protein expression and purification and/or
single-particle cryoEM. Good communication & organizational skills and the
ability to work independently are important for this position. Salary will
be commensurate with the candidate's experience, and will be based on the
NIH postdoctoral stipend scale.

The Petrou Lab is located in Newark, New Jersey - 20 minutes away from New
York city! The Rutgers New Jersey CryoEM/ET facility, located in
Piscataway, New Jersey, provides access to cryoEM and cryoET
instrumentation, including a 200kV Talos Arctica microscope, an Aquilos 2
FIB-SEM microscope, and a Leica cryo-CLEM setup. In addition, a local
cryoEM facility at NJMS equipped with a 100kV Tundra microscope and
speed-enhanced Ceta camera will begin operating in the next few months, and
is located in the same building as the Petrou Lab.

Interested candidates can find additional details and apply online at:
https://jobs.rutgers.edu/postings/182250

A short cover letter, CV and contact information for three references are
required. Candidates will be evaluated on a rolling basis until the
position is filled.

For further information, candidates can contact Dr Petrou via email (
vasileios.pet...@rutgers.edu) or direct message on Twitter
(@VasileiosPetrou) or LinkedIn.


Regards and best wishes,
Ankita

Postdoctoral Fellow, Petrou Lab
Department of Microbiology, Biochemistry and Molecular Genetics, and Center
for Immunity and Inflammation, Rutgers New Jersey Medical School
225 Warren Street
Newark, NJ 07103



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/