[ccp4bb] problem with typing characters into ccp4interface 8.0.011

[Alex Aleshin]

This morning I've discovered that I cannot type any character (numbers are 
fine) into CCP4I command windows. I've upgraded the package to a 8.0.011 
version, but it did not help. Could anybody advise what might happen and how to 
fix it?

Regards,
Alex   





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[ccp4bb] Senior Scientist position available in Structural Biology within SANOFI (Cambridge Massachusetts)

[eduardo Bruch]

Dear all,



Our Structural Biology group within SANOFI (Cambridge Massachusetts) has an
opening for a Senior Scientist (Job ID: R2695834) and we are seeking a
highly motivated scientist with a solid background in structural biology
and strong hands-on experience in CryoEM.



If you are interested in applying for this position, please follow the link
provided below.



Thanks in advance for your interest!

Best

Eduardo Bruch



https://sanofi.wd3.myworkdayjobs.com/SanofiCareers/job/Cambridge-MA/Senior-Scientist_R2695834



Senior. Scientist - U.S. IDD structural biology

We are looking for a highly motivated scientist to join our structural
biology group at Sanofi in Cambridge MA.  As a key member of our dynamic
team, you will be responsible for determining critical structural biology
data through both cryo-electron microscopy and x-ray crystallography;
actively pursuing solutions for unmet medical needs in diverse therapeutic
areas and collaborating with multidisciplinary teams within Sanofi in
Cambridge, US, Frankfurt, Germany and Paris, France. The successful
candidate will excel in a fast-paced, highly diverse discovery environment,
will have a strong focus on scientific rigor, have proven success in
organized and independent work, and an exceptional attention to detail.
Applicants who are passionate about structural biology are encouraged to
apply.

Candidate profile:

·   CryoEM expert scientist that can independently design and carry out
EM experiments and interpret results (sample preparation, data collection,
data processing and solving structures). Analyze interactions and propose
structure-based improvements for small-molecule drug discovery. Enable
building state-of-the art technologies in related areas to enhance research
activities.

·   Work closely with Sanofi digital to automate CryoEM data collection
processes to evaluate samples in medium-throughput manner. Python or other
programming languages for building pipelines for data collection and
processing is a plus.

·   Share responsibility for maintaining the Glacios cryo-electron
microscope (beam alignment, calibration, cryo-cycling, etc.).

·   Expertise with all related softwares (CryoSparc, SerialEM, Relion,
cisTEM, Chimera, Eman2, Coot, phenix, ccp4 suite etc.).

·   Provide expertise to project teams pursuing different drug
modalities at Sanofi.

·   Manage and deliver on projects in a timely fashion.

·   Train new users on finer aspects of CryoEM grid preparation and
data collection when necessary.

·   Experience in X-ray crystallography is a strong plus. The candidate
will be expected to train to support this area in case of no prior
experience.

·   Experience in expression and purification strategies using
bacterial, insect, and mammalian hosts and membrane protein purification.
The candidate should be capable of purifying protein for the structural
biology group when needed.

·   Experience in biophysical characterization (SPR, DSF, MST etc.) is
a plus.

·   Have excellent communication skills. Should be able to clearly
articulate data, project strategies both internally and externally.

Qualifications:

·   PhD with 3+yrs of postdoctoral and/or industry experience in
Structural Biology, Biophysics, Protein Biochemistry or related discipline.

·   Strong experience in cryo-EM is required.

·   The ideal candidate should be detail-oriented, organized and
demonstrate good lab practices.

·   Must be a collaborative team player with strong communication
skills.

Sanofi Inc. and its U.S. affiliates are Equal Opportunity and Affirmative
Action employers committed to a culturally diverse workforce. All qualified
applicants will receive consideration for employment without regard to
race; color; creed; religion; national origin; age; ancestry; nationality;
marital, domestic partnership or civil union status; sex, gender, gender
identity or expression; affectional or sexual orientation; disability;
veteran or military status or liability for military status; domestic
violence victim status; atypical cellular or blood trait; genetic
information (including the refusal to submit to genetic testing) or any
other characteristic protected by law.

As a healthcare company and a vaccine manufacturer, Sanofi has an important
responsibility to protect individual and public health. All US based roles
require individuals to be fully vaccinated against COVID-19 as part of your
job responsibilities.

According to the CDC, an individual is considered to be “fully vaccinated”
fourteen (14) days after receiving (a) the second dose of the Moderna or
Pfizer vaccine, or (b) the single dose of the J vaccine. Fully
vaccinated, for new Sanofi employees, is to be fully vaccinated 14 DAYS
PRIOR TO START DATE.

#GD-SA
#LI-SA

At Sanofi diversity and inclusion is foundational to how we operate and
embedded in our Core Values. We recognize to truly tap into the richness
diversity brings we must lead 

[ccp4bb] A new process for aggregating and naming assemblies in the PDB

[David Armstrong]

Dear ccp4bb,

PDBe has created a new process to aggregate and name assemblies in the 
PDB based on unique assembly composition. This process allows assemblies 
with the same composition to be aggregated together. The assemblies can 
be aggregated into over 90,000 distinct compositions by mapping each 
component in an assembly to external databases. Over 90% of the 
assemblies have been named using external resources such as Complex 
Portal, Gene Ontology, UniProt and manual curation by PDBe annotators.


This new process will allow researchers to find all assemblies that have 
a certain UniProt/Rfam accession or combination of accessions. Users can 
also find super-assemblies of an assembly which can help understand how 
different protein complexes interact with each other. Finally, users can 
find assemblies based on specific names helping to identify and study 
specific protein complexes that are relevant to their research.


Find out more at 
https://www.ebi.ac.uk/pdbe/news/new-process-aggregating-and-naming-assemblies-pdb 



Kind Regards,
David

--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK



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[ccp4bb] computational scientist sought

[Jennifer Fleming]

Dear all,

we are seeking a computational scientist to integrate the 
multidimensional scaling program, PaSiMap, and its underlying 
cc_analysis pipeline (references below) into the sequence alignment 
viewer Jalview. This integration will advance the flexibility of PaSiMap 
in testing suitable identity matrix for the best clustering of sequence 
sets. The work is within the context of an existing collaboration 
between the laboratories of Prof Kay Diederichs, Prof Olga Mayans and Dr 
Jennifer Fleming at the University of Konstanz.


For this post, Java experience is essential. Background in biological 
informatics is desirable, but not a pre-requisite.
The position is available at 50% for 4 months (July-October). Because of 
the limited hiring period, the position is better suited to candidates 
already located in our geographical area. Candidates must have completed 
a Master degree in a suitable discipline and have demonstrated 
capabilities in this area.


  Applications must be in the form of a CV, degree transcripts and a 
short letter describing existing expertise.


  Applications and informal enquiries are to be directed to: 
jennifer.flem...@uni-konstanz.de


Best Regards,

Jennifer Fleming

-

http://pasimap.biologie.uni-konstanz.de

Su K, Mayans O, Diederichs K and Fleming JR (2022) PaSiMap: Pairwise 
sequence similarity mapping with PaSiMap: reclassification of 
immunoglobulin domains from titin as case study. Computational and 
Structural Biotechnology Journal.


PaSiMap/ cc_analysis applications:

Zacharchenko T, Dorendorf T, Locker N, van Dijk E, Katzemich A, 
Diederichs K, Bullard B, Mayans O. (2023). PK1 from Drosophila obscurin 
is an inactive pseudokinase with scaffolding properties. Open Biology. 
2023 Apr;13(4):220350.  doi: 10.1098/rsob.220350.


Hunkler S, Diederichs K, Kukharenko O, Peter C. Fast conformational 
clustering of extensive molecular dynamics simulation data. J Chem Phys. 
2023 Apr 14;158(14):144109. doi: 10.1063/5.0142797.


--
Dr Jennifer Fleming
DFG Investigator
Fachbereich Biologie
Universität Konstanz
78457 Konstanz
Germany

Email: jennifer.flem...@uni-konstanz.de



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[ccp4bb] wwPDB NEWS: ls-lR index file to be removed July 12, 2023

[Deborah Harrus]

Dear all,

With continuing growth of the PDB archive, the size of the file that 
lists all directory contents 
(currentlyhttps://files.wwpdb.org/pub/pdb/ls-lR) will become a challenge 
for long term maintenance. wwPDB will remove this file from the PDB 
archive at 00:00 UTC on July 12, 2023. We strongly encourage users to 
utilize filespreviously announced 
that 
containing the same data (https://files.wwpdb.org/pub/pdb/holdings/).


These inventory data files offer a quick overview of data in the 
archive. Two new inventory files for experimental data are added. These 
files are in the extensible JSON format, and can be found under the new 
/pdb/holdings/ archive tree.


The inventory lists provided include:

 * current_file_holdings.json.gz: a list of released PDB entries and
   the file types present for each in the PDB Core Archive (e.g.
   coordinate data, experimental data, validation report).
 * refdata_id_list.json.gz: a list of released chemical reference
   entries, their content types (e.g., Chemical Component, BIRD), and
   the most recent modification date of the reference file.
 * released_structures_last_modified_dates.json.gz: a list of released
   PDB entries with the most recent modification date of the PDBx/mmCIF
   file.
 * released_experimental_data_last_modified_dates.json.gz: a list of
   released experimental data files with the most recent modification date
 * obsolete_structures_last_modified_dates.json.gz: a list of obsoleted
   PDB entries with the most recent modification date of the PDBx/mmCIF
   file.
 * obsolete_experimental_data_last_modified_dates.json.gz: a list of
   obsoleted experimental data files with the most recent modification
   date.
 * all_removed_entries.json.gz: a list of obsoleted PDB entries
   including information for entry authors, entry title, release date,
   obsolete date, and superseding PDB ID, if any.
 * unreleased_entries.json.gz: a list of on-hold PDB entries, their
   entry status, deposition date, and pre-release sequence information,
   where available.

Users are encouraged to utilize these inventory files. For example, 
checking for the update of the PDB archive can be performed 
usingcurrent_file_holdings.json.gz 
orreleased_structures_last_modified_dates.json.gz 
in 
/pub/pdb/holdings/.


Please contactinfo@wwpdb.orgwith any questions.

Read this news online: 
https://www.wwpdb.org/news/news?year=2023#645bbfdd1d621d75127a7a48


Kind regards,

Deborah Harrus

PDBe

--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
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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