[ccp4bb] More efficient delivery of sequence cluster files

[Jose Duarte]

The sequence cluster files offered at RCSB PDB's CDN server (see
https://www.rcsb.org/docs/programmatic-access/file-download-services#sequence-clusters-data)
are now offered using PDB polymer entity identifiers, removing much
redundancy and producing smaller file sizes. The previous chain-based
cluster files will be updated only until April 12 2022. If you use these
files, please consider migrating to the entity-based files as soon as
possible.

Please also note that more integrated access to the same data is available
via RCSB PDB's Data and Search APIs. See:

https://data.rcsb.org/#gql-example-3
https://search.rcsb.org/#dealing-with-redundancy

Best wishes

Jose

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center
UC San Diego



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Re: [ccp4bb] 2022 S2C2 High Resolution CryoET Image Processing Virtual Workshop March 1-3, 2022 8:00 AM - 2:00 PM (PST)

[Polizzi, JoAnn]

Good morning All,

With two weeks left until our 2022 S2C2 High Resolution CryoET Image Processing 
Workshop, I wanted to send a reminder that if you have not done so yet please 
fill in an application for the workshop.  I will close the registration site 
down on February 19, to complete the processing of our applicants.  The 
workshop page link with more information and registration page can be found 
below.

Best,
JoAnn

From: Polizzi, JoAnn 
Sent: Wednesday, January 19, 2022 11:01 AM
To: 3...@ncmir.ucsd.edu; cc...@jiscmail.ac.uk; CCP4BB@JISCMAIL.AC.UK; 
cryoem-announce 
Cc: Polizzi, JoAnn 
Subject: 2022 S2C2 High Resolution CryoET Image Processing Virtual Workshop 
March 1-3, 2022 8:00 AM - 2:00 PM (PST)

Dear CryoEM Community,

We are pleased to announce that we will be hosting a 3-day virtual workshop on 
High Resolution CryoET Image Processing on March 1-3, 2022. The expert speakers 
will lecture on the basic principles and practical usage of software for image 
processing and analysis of high resolution cryoET data.

Our list of speakers includes David DeRosier, Frederick Sigworth, Tom Goddard, 
Steven Ludtke, Dimitry Tegunov.
For more information and the registration link, please go to our S2C2 CryoEM 
Workshop
 page.

Organizer: Wah Chiu, Stanford University

The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.



[cid:image002.png@01D82189.8559F150]
JoAnn Polizzi | Administrative Assistant, SSRL Directorate
Biosciences and CryoEM & Bioimaging Divisions
SLAC National Accelerator Laboratory | Menlo Park, CA
p: 650.926.3357 | m: 408.772.5379
e: joa...@slac.stanford.edu | w: 
slac.stanford.edu

You can't go back and change the beginning but you can start where you are and 
change the ending.  James Sherman (Rejection, 1982)





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[ccp4bb] Reminder: CBMS Lecture Series: Wednesday February 16, 13:30 pm (NY time zone)

[Stojanoff, Vivian]

You are cordially invited to join  the Center for Biomolecular Structure 
Lecture Series ………..





Jochen Hub

Universität des Saarlandes



WEDNESDAY, February 16, 13:30 (EST)





"Structure and ensemble refinement against SWAXS data with explicit-solvent MD 
simulations"



Register in advance for this meeting:



 https://bnl.zoomgov.com/meeting/register/vJItc-yvqj4uG9ryjG2Se_JF3fZh5MJQgQc



Abstract:

Small-angle and wide-angle X-ray scattering in solution (SAXS, WAXS, SWAXS) is 
an increasingly accurate method for obtaining structural information on 
biomolecules and soft-matter complexes in solution. However, the interpretation 
of the solution scattering data by computational methods is complicated by (i) 
the low information content of the data and (ii) by scattering contributions 
from the hydration layer and excluded solvent, leading to a significant risk of 
over interpretation upon fitting structural models against SWAXS data.To 
overcome such problems, we have developed methods for interpreting SWAXS data 
with all-atom explicit-solvent molecular dynamics (MD) simulations. In this 
talk we show how  MD simulations aid the interpretation of SWAXS data in 
multiple manners: The physical information in atomistic force fields 
complements the low information SWAXS data; explicit-solvent MD is used to 
predict solvent scattering contributions, and the MD-related sampling methods 
may guide the structure refinement against SWAXS data.



==



Vivian Stojanoff, PhD

Education, Training, Outreach

User Program

p 1(631) 344 8375

e nsls.lifescien...@gmail.com

w https://www.bnl.gov/ps/lifesciences/



Address:

Center for Biomolecular Structure

National Synchrotron Light Source II

Building 745

Brookhaven National Laboratory

Upton NY 11973




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[ccp4bb] Postdoctoral position in structural bioinformatics at RCSB @ UCSF

[Ben Webb]

Dear colleagues,

The research group of Andrej Sali at UCSF (https://salilab.org) is 
seeking a highly motivated postdoctoral researcher in bioinformatics, 
with domain experience in structural biology. The candidate should be 
interested in structural biological data and enjoy engaging with other 
programmers and scientists in a collaborative team environment. The 
position is part of the RCSB Protein Data Bank (https://rcsb.org) effort 
at University of California, San Francisco, focused on the development 
of resources for the integrative methods initiative of worldwide Protein 
Data Bank. The effort has already produced a number of scientific 
publications, and is expected to provide ample opportunities for 
additional first-author publications in the future, including in 
Bayesian validation of structural models in general, one of the 
frontiers in structural biology.


Responsibilities:

  - Design, development, and deployment of the nascent archive for
integrative structures at the Protein Data Bank, PDB-Dev
(https://pdb-dev.wwpdb.org)
  - Integration of complex bioinformatics data, implementation of
specialized algorithms for search/data analysis and use of AI tools
  - Design and implementation of cloud-ready deployments usin
containerization and modern cloud technologies
  - Analysis, refactoring and adaptation of legacy code to conform to
new architecture designs
  - Debugging, testing, troubleshooting

Qualifications:

  - PhD in Computer Science, Biochemistry, Bioinformatics, or a related
discipline, or a comparable combination of education and experience
developing modern scientific data applications
  - Excellent interpersonal, verbal, and written communication skills
  - Experience with Python, document databases, search and data access
tools

Scientific background in any of the following areas would be considered 
a major plus: Molecular Biology, Bioinformatics, Cheminformatics, 
Biochemistry, Chemistry, Genomics. Experience working with large and 
complex scientific datasets would also be considered a plus.


Outstanding Benefits Package. UCSF is a friendly and collaborative 
working environment with excellent professional development 
opportunities. There are personal rewards including a comprehensive 
health plan.


About the Sali research group at UCSF: https://salilab.org.

About RCSB PDB: The work at RCSB PDB (https://rcsb.org) focuses on data 
analysis, integration, and transformation, and the presentation and 
visualization of data using complex interactive graphical user 
interfaces. An important aspect is to provide users with the ability to 
search and explore the PDB data archive. Solutions are implemented using 
a wide range of components developed and maintained in-house, in 
addition to third-party tools, libraries, frameworks and technologies. 
The candidate should be comfortable working in a dynamic environment, 
and able to demonstrate an ability to think creatively, generate new 
ideas, and implement solutions. The candidate should also show an 
eagerness to learn new skills and technologies.


Apply: Please send an email with a cover letter and cv to Andrej Sali at 
s...@salilab.org.




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[ccp4bb] Graphical output running CCP4i on Windows 10

[Andreas Heine]

Hi,

I installed ccp4i on Windows10. Here, the graphical output is not 
working anymore. Are the any add-ons I need to install (eg dbviewer)?


Any advice is greatly appreciated.

Andreas



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[ccp4bb] Multiple Protein Sciences / Structural Biology Scientist Roles at Schrödinger (Boston, MA)

[Enrico Malito]

Hello,

At Schrödinger (https://www.schrodinger.com/), we are seeking outstanding and 
highly motivated scientists to work on structure-based drug discovery in our 
new labs in Natick, MA, just outside of Boston (https://xtalbiostructures.com/).

If you are interested in i) joining a cross-functional group of scientists and 
drug developers with experience working on all common target classes and 
therapeutic areas, ii) using breakthrough computational methods, and iii) 
contributing to our rapidly expanding portfolio of drug discovery programs and 
collaborations, please apply following the links provided below.



Principal Scientist/Lab Head - Protein Sciences 
https://boards.greenhouse.io/schrdinger/jobs/4924812003?gh_src=cd0d760c3us. 

Key responsibilities:
Implement and oversee gene-to-protein capabilities for structural biology 
applications.
Establish, perform, and oversee experimental protocols and tasks in the areas 
of molecular biology (gene construct design), protein expression (using 
mammalian, insect, bacterial cell systems), and protein purification.



Senior Scientist - Protein Biochemistry and Biophysics / Structural Biology 
https://boards.greenhouse.io/schrdinger/jobs/4924506003?gh_src=839a2b363us

Key responsibilities:
Contribute to construct design and expression of proteins in multiple host 
species (E. coli, insect, mammalian).
Perform protein purification for structural biology applications (X-ray 
crystallography and cryo-EM).
Perform protein characterization using biophysical methods (ITC, SPR, TSA, 
etc.).
Perform protein crystallization and grid preparation for X-ray crystallography 
and cryo-EM.



Scientist - Protein Production Specialist 
https://boards.greenhouse.io/schrdinger/jobs/4924817003?gh_src=13238cf73us

Key responsibilities:
Work on a gene-to-protein pipeline for structural biology applications.
Perform experimental procedures in the areas of molecular biology (gene 
construct design) and protein expression using different cell systems 
(mammalian, insect, bacterial).




Best regards,

Enrico Malito
Executive Director, Structural Biology
Schrödinger, NY, USA



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[ccp4bb] Postdoc / PhD posts available: University of Oxford (kinase crystallography)

[Alex Bullock]

My group has 3 posts in advertising right now on protein kinase crystallography 
at the Centre for Medicines Discovery, University of Oxford, UK:

155976 -Postdoctoral Scientist - Receptor Kinase Structural Biology
Job Details 
(corehr.com)

155977- Postdoctoral Scientist - CDK Kinase Structural Biology
Job Details 
(corehr.com)

Funded PhD post (Graduate Scholarship) on ACVR1 kinase/FOP
Link  
here

Informal enquires can be made to 
alex.bull...@cmd.ox.ac.uk
Thanks
Alex.
https://www.cmd.ox.ac.uk/team/alex-bullock





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[ccp4bb] Exascale and ExCALIBUR Webinar

[Sarah Fegan - STFC UKRI]

Dear CCPBioSim and Bioscience colleagues,


CCPBioSim are very excited to be hosting the online seminar “ExCALIBUR 
Programme: Progress and Upcoming Calls” by Elizabeth Bent from EPSRC and "UK 
Exascale Supercomputer Project: Plans and Opportunities" Mark Parsons from 
EPCC. The seminar will take place on 2 March 2022 at 13:30 British time. The 
details and registration link can be found at 
https://www.ccpbiosim.ac.uk/excalibur2022. The registration deadline is 28 
February 2022.



This seminar is aimed at UK bioscientists who rely on computation for their 
research. The exciting potential of exascale computing for biosciences is that 
it offers us 1000 fold more capability, but there are challenges to be 
overcome, as Mark will explain. Elizabeth will describe the UKRI aspirations 
for exascale, and how they will support us.



We very much hope that you can join us for the talk and for the discussion 
afterwards!

Sarah Harris, Mark Parson, Elizabeth Bent.


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 
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[ccp4bb] Multiple Structural & biophysical roles at GSK R, Stevenage, UK

[Chun-wa Chung]

Title : Multiple Structural and Biophysical Scientists Roles at GSK R, 
Stevenage,UK.

As we continue to grow this area we have multiple openings for talented 
structural & biophysical scientists to join GSK's UK Structural & Biophysical 
Sciences group at Stevenage.
This is an opportunity to join a multi-disciplinary department that provides 
molecular insights into both small molecule and biopharmaceutical drug 
discovery.
Two roles are already posted and due to close on the 21st Feb.
319896 Structural Mass Spectrometry - with membrane protein experience
https://jobs.gsk.com/en-gb/jobs/319896?lang=en-us=en-GB

321550 Cryo-EM Scientist - processing expert
https://jobs.gsk.com/en-gb/jobs/321550?lang=en-us=en-GB

Our expansion means a few more openings will be coming out shortly, so please 
do have a look and apply if the prospect of joining us excites you.

Thanks for reading this.
Best wishes,
Chun-wa


Chun-wa Chung
UK Head Structural & Biophysics  Sciences
GlaxoSmithKline R
Stevenage
SG1 2NY
 email : chun-wa.h.ch...@gsk.com



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