[ccp4bb] PDBe Coordinator Position at EMBL-EBI

via PDBe data resources, tools and services. The closing date for this post is 22nd September 2023. For more information and to apply, visit: https://www.embl.org/jobs/position/EBI02160 Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute

[ccp4bb] Introducing ‘Covalently Linked Components’ and enriched ligand information at PDBe

ve our data infrastructure and user accessibility. Thankyou for your continued support. 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

[ccp4bb] PDBImages: A new, open-source macromolecular structure imaging pipeline

;https://github.com/PDBeurope/pdb-images>). Read more: https://www.ebi.ac.uk/pdbe/news/pdbimages-new-open-source-macromolecular-structure-imaging-pipeline <https://www.ebi.ac.uk/pdbe/news/pdbimages-new-open-source-macromolecular-structure-imaging-pipeline>* -- David Armstrong Outreach and

[ccp4bb] 3D-Beacons update: Search for structural models by protein sequence

quence 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 To

[ccp4bb] Clustering of distinct protein conformations across the whole PDB archive

r would like further details, please feel free to contact the team at pdbeh...@ebi.ac.uk. Kind regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton C

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

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

Re: [ccp4bb] choosing an NMR structure from PDB

p;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/ -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI

[ccp4bb] Removal of ls-lR index file from the PDB archive

/holdings/released_structures_last_modified_dates.json.gz> in /pub/pdb/holdings/. Please contact i...@wwpdb.org with any questions. -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge

[ccp4bb] Updated pipeline for small molecule data processing at PDBe

://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe <https://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe> Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EM

[ccp4bb] Helping improve AlphaFold DB - survey on similarity searches

our time and interest! As we progress on this project, we will keep the community updated. * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge

[ccp4bb] Enriched chemical component files at PDBe

generated using RDKit in these updated CCD files. Kind Regards, David Armstrong -- 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

[ccp4bb] Reminder: AlphaFold DB bioinformatics training role at EMBL-EBI - deadline 15th Jan

licly represent AlphaFold DB at various training events. There is the option for a part time role in this position. Deadline: 15th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs. Kind Regards, David Armstrong * -- David Armstrong Outreach and Training

[ccp4bb] Software Infrastructure Engineer role available at PDBe

-KB services remain firmly placed on a sustainable footing. Deadline: 29th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs Kind Regards, David * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European

[ccp4bb] AlphaFold DB bioinformatics training role available at EMBL-EBI

and publicly represent AlphaFold DB at various training events. There is the option for a part time role in this position. Deadline: 15th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs. Kind Regards, David Armstrong * -- David Armstrong Outreach and Tra

[ccp4bb] Multiple AlphaFold DB jobs available at EMBL-EBI

part time role in this position. Deadline: 26th September 2022 For more information on all these job roles and to apply, visit https://pdbe.org/jobs. * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wel

[ccp4bb] Improved EM validation with Q-score at the PDB

map+model, EM map-only, and EM tomograms. If you have any questions or queries about wwPDB validation, please contact us at validat...@mail.wwpdb.org. Best regards, James Tolchard -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular

Re: [ccp4bb] Off-topic: Mol* Viewer re-centring hack

entation at PDBe and queries about the use of the viewer. Kind Regards, David Armstrong On 28/06/2022 10:36, Read, Jon wrote: I have been using Mol* recently which looks like a really nice tool for basic model viewing. When you click off an atom (which is the normal action for clearing a select

[ccp4bb] Reminder: Data Visualisation Software Engineer position at PDBe

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 Tel: +44 1223 492544

[ccp4bb] Reminder: Bioinformatician/Scientific Programmer position at PDBe

user-facing web pages for PDBe and PDBe-KB. The closing date for this post is 3rd May 2022. For more information and to apply, visit: https://www.embl.org/jobs/position/EBI02000 Kind Regards, David Armstrong -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute

[ccp4bb] Bioinformatician/Scientific Programmer position at PDBe

more information and to apply, visit: https://www.embl.org/jobs/position/EBI02000 Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton

[ccp4bb] Bioinformatician position at PDBe - closing Friday

/pdbe/about/jobs Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544

[ccp4bb] Deposition of half-maps for certain EM entries now mandatory for EMDB deposition

or the affected modalities to implement support for output of such half-maps (if this is not already available). Any queries about this policy change can be directed to i...@wwpdb.org. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinfor

[ccp4bb] PDBe updated mmCIF files now available via FTP

ilable at https://www.ebi.ac.uk/pdbe/download/api. If you have any queries about these files or how to access them, please contact our helpdesk at pdb...@ebi.ac.uk. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EM

[ccp4bb] Distributing PDBx/mmCIF Formatted Assembly Files at the PDB Core Archive

for improved efficiency. For any further information please email i...@wwpdb.org. <mailto:i...@wwpdb.org> Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellco

[ccp4bb] Software Engineer position at PDBe

Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544

[ccp4bb] Bioinformatician position at PDBe - deadline extended to 9th Feb

the University of Edinburgh. The closing date for this post has been extended to 9th February 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI01913 Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European

[ccp4bb] Reminder: Bioinformatician position at PDBe - closing soon

the University of Edinburgh. The closing date for this post is 26th January 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI01913 Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics

[ccp4bb] SIFTS sequence mappings now included in PDBe mmCIF files

tly retrieved from these files and are available from PDBe entry pages. For more information, visit https://www.ebi.ac.uk/pdbe/about/news/sifts-data-now-included-pdbe-mmcif-files Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics I

[ccp4bb] Bioinformatician position at PDBe

the University of Edinburgh to facilitate deposition of cross-linking data during PDB structure deposition. The closing date for this post is 26th January 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI01913 Kind regards, David Armstrong

[ccp4bb] REMINDER: Bioinformatician position at PDBe - closing 4th November

team at the University of Edinburgh to facilitate deposition of cross-linking data during PDB structure deposition. The closing date for this post is *4th November 2021*. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI01913 Kind regards, David -- David

[ccp4bb] Abstract submission deadline: 15th September - "50 Years of PDB" EMBL conference

ines * Genomics meets structural biology * The next 50 years: future perspectives *Register and submit an abstract for the conference at s.embl.org/pdb21-01* Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Insti

[ccp4bb] Extended PDB IDs and PDB DOIs now available in PDBx/mmCIF files

iew code and remove related limitations. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44

[ccp4bb] Reminder: Bringing Molecular Structure to Life: 50 Years of the PDB closes abstract submission soon

Sponsor this event <mailto:sponsors...@embl.de> Sponsor this event <mailto:sponsors...@embl.de> Download the poster <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab&id=72f55264e0&e=848f463a70> Download the poster <https://embl.us13.list-manage.com

[ccp4bb] Bringing Molecular Structure to Life: 50 Years of PDB - an EMBL conference

ique or media, however, we will require a high-resolution image of the artwork for display in the virtual exhibition. Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Labora

Re: [ccp4bb] generate symmetry mates of EM structures

mCIF files containing the full assemblies. In this case, "Assembly 1 (mmCIF; gz)" would give you the full structure. Kind Regards, David Armstrong On 21/05/2021 11:33, Xiao Lei wrote: Dear Community, I wonder if there is a way to generate symmetry mates of EM structures? For example

Re: [ccp4bb] PDBe cif directories

CIF files, however also include additional categories output from the PDBe CCD utils process (a wrapper of RDKit), including chemical properties and external cross reference mappings. If you have any further questions, please let us know at pdbeh...@ebi.ac.uk Kind Regards, David Armstrong On 04

[ccp4bb] Please help us improve our PDBe-KB aggregated views of proteins

ffer. If you have any questions, please feel free to contact us directly. Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge C

[ccp4bb] EMBL-EBI Structural Bioinformatics course (virtual) - Registration extended until 2nd October

. This course will be a virtual event delivered via a mixture of live-streamed sessions, pre-recorded lectures, and tutorials with live support. For more information and to register, please visit bit.ly/EBI_sbr Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator

[ccp4bb] Help us design PDBe-KB's aggregated views of small molecules

yKUU5hwE9>. The full link to this feedback form is provided below: https://forms.gle/4Kk5kWLDyKUU5hwE9 Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust G

[ccp4bb] Reminder - PDBe workshop: Making the most of PDB data with PDBe’s new graph database

tabase <http://www.ebi.ac.uk/training/events/2020/mining-pdbe-and-pdbe-kb-using-graph-database>. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Ca

[ccp4bb] PDBe workshop: Making the most of PDB data with our new graph database

-graph-database <http://www.ebi.ac.uk/training/events/2020/mining-pdbe-and-pdbe-kb-using-graph-database>. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome

Re: [ccp4bb] Improve your previously released coordinates with OneDep

ing structures can benefit from re_do's, etc, but I would like to preserve the original PDB-IDs, as published, and I don't want to spend too long on it! Thank you, Jon.C. On Thursday, 1 August 2019, 09:34:40 BST, David Armstrong wrote: Dear CCP4BB, T

[ccp4bb] Improve your previously released coordinates with OneDep

data. PDB versioning will be limited to one replacement per PDB entry per year, and three entries per Principal Investigator per year. For more, please visit the wwPDB news pages <https://www.wwpdb.org/news/news#5d3ef68aea7d0653b99c87fd>. -- David Armstrong Outreach and Training Coord

[ccp4bb] Survey on EMBL-EBI's data resources (incl. PDBe, PDBe-KB, EMDB, EMPIAR, BioImage Archive)

cular, cellular, and beyond). The survey can be found here: https://www.surveymonkey.co.uk/r/2N99899 Please feel free to pass this email on to others who may have an interest in EMBL-EBI's data resources. Many thanks, David Armstrong -- David Armstrong Outreach and Training Coordinator PDB

[ccp4bb] REMINDER: Scientific Data Curator position (PDB and EMDB)

Dear CCP4BB, Just a gentle reminder of the scientific data curator position available at PDBe. The closing date for the post is Friday 5th July. For more information, please see: https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01403 Kind Regards, David Armstrong On 29/05/2019 08

[ccp4bb] New PDBe-KB aggregated views of protein structure

ce in a way that is most valuable for you all. If you would like more information about the new resource then please visit the PDBe-KB website <https://www.ebi.ac.uk/pdbe/pdbe-kb> or view our webinar <https://youtu.be/ZJksQS4vmuM>, which introduces you to our new pages. Many th

[ccp4bb] Wednesday 3.30pm (UTC) - Webinar: PDBe-KB Aggregated views

visit the following link: bit.ly/PDBe-KB-webinar Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223

[ccp4bb] Fwd: 2 EMDB Job Opportunities at EMBL-EBI

Please see the following job opportunities available with our colleagues at EMDB. Kind Regards, David Armstrong Forwarded Message Subject:2 EMDB Job Opportunities at EMBL-EBI Date: Tue, 22 Jan 2019 10:46:19 + From: Osman Salih To: 'David Arms

Re: [ccp4bb] RNA pdb molecular weight

?SUBED1=CCP4BB&A=1 -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 49