[ccp4bb] Powerful new search from pdbe.org

, whether or not the paper describing that code is cited. At 10am UK time on the 21st July we will be presenting a webinar demonstrating these new features of the PDBe website. To sign up visit the link below https://attendee.gototraining.com/r/8145177008665955586 Regards John -- John Berrisford

Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities

in the PDB header for everything in mmCIF but I do for the reverse case). Thanks Phil Jeffrey Princeton -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223

[ccp4bb] PDBe webinar - 3D visualisation in your browser

ac.uk/pdbe/about/news/pdbe-brings-electron-density-viewing-masses -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 http://www.pdbe.org http://www.fa

[ccp4bb] Major PDB FTP archive update to V5.0

uld be sent to deposit-h...@mail.wwpdb.org. Regards John * -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 http://www.pdbe.org http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Scienc

[ccp4bb] Software Engineer / Bioinformatician position at PDBe

and ChEMBL teams, all co-located at the EBI. For more details and to apply, please see the listing on the EMBL careers site (https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_00941) Application deadline is 13th August 2017 Regards John -- John Berrisford PDBe European Bioinformatics

[ccp4bb] PDBe Software Engineer / Bioinformatician

he 9th July 2017. Thanks John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 http://www.pdbe.org http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope

[ccp4bb] PDBe API webinar 4th July 2017

of the EBI API webinar series. The following link provides a link to registration for the PDBe webinar and access to previous webinars in the EBI series. http://www.ebi.ac.uk/training/events/2017/embl-ebi-programmatically-take-rest-manual-searching-webinar-series Regards John -- John

Re: [ccp4bb] AW: [ccp4bb] question regarding sequence numbering

replication stress response <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nature.com_articles_ncomms15847=DwMFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU=ajttqwr7ED8_WBG6ALc86GNNTa7qa_WbddCP5A

Re: [ccp4bb] PDB search help

Dear Rajesh This is possible with our search API See: http://www.ebi.ac.uk/pdbe/api/doc/search.html For example https://www.ebi.ac.uk/pdbe/search/pdb/select?q=pfam_name:Lipocalin =json then for each

[ccp4bb] A clearer 3D view of sugars

-sugars for further details John PDBe -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 http://www.pdbe.org http://www.facebook.com/proteindatabank http

[ccp4bb] Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management

b/data/structures/ will continue to use the familiar naming style and will continue to contain only the latest version for every entry. John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridg

[ccp4bb] EBI moving to HTTPS access

at you have to change any programmatic requests to HTTPS. I'm really sorry for the short notice, but we only received very short notice of the change. Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory We

Re: [ccp4bb] Removing a ter line present in the middle of the chain

he pdb spec from the PDB requires (HETATM for all non-standard residues). Example: https://files.rcsb.org/view/5ABS.pdb Marcin -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel:

Re: [ccp4bb] LINK vs LINKR

+43 767 571 0536 -- Many plausible ideas vanish at the presence of thought -- -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Tru

Re: [ccp4bb] LINK vs LINKR

and forgetting to leave useless CISPEP SSBOND LNK etc lines in the header... Eleanor On 10 December 2017 at 19:59, John Berrisford <j...@ebi.ac.uk <mailto:j...@ebi.ac.uk>> wrote: Dear Bernhard When we convert from PDB to mmCIF we do indeed ignore LINKR records as these are

Re: [ccp4bb] LINK vs LINKR

ck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediat

[ccp4bb] PDBe Scientific Programmer / Bioinformatician

e data and sequence information from UniProt and other databases. For more details and to apply, please see the listing on the EMBL careers site. <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01224> Application deadline is 24th June 2018 John -- John Berrisford PDBe European Bi

[ccp4bb] Improvements to onedep deposition system

For depositors who subunit replacements after curation of their entries, the new version of wwPDB OneDep system improves this process. This updated process ensures that all new data are checked and validated before the new files are merged into the deposition session. A new validation report

[ccp4bb] Exciting new updates at PDBe

You might have noticed some changes on the PDBe website today as we’ve introduced some great improvements to the search options and new features on our entry pages. All these changes should help you to find what you’re looking for in the PDB archive and give you better biological context for

[ccp4bb] Reminder - PDBe Scientific Programmer / Bioinformatician

Reminder: The deadline for applications to this post is the 24th June 2018. Regards John From: CCP4 bulletin board On Behalf Of John Berrisford Sent: 21 May 2018 13:57 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PDBe Scientific Programmer / Bioinformatician PDBe are looking

[ccp4bb] Highlighting RNA in a protein world

system and entry pages. For more details see our news item at <https://www.ebi.ac.uk/pdbe/about/news/highlighting-rna-protein-world> https://www.ebi.ac.uk/pdbe/about/news/highlighting-rna-protein-world John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) Eu

[ccp4bb] Data Enrichment and Integration Coordinator at PDBe

of biomacromolecular structure data and tools for its delivery. For further details, and to apply, please follow the link http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj=56236=15470 <http://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj=56236=15470>. -- John Berrisford PDBe European Bioinfor

Re: [ccp4bb] Regarding symmetry notion in coot

>From a PDB deposition point of view, I echo Paul’s comment. If possible, >please move your molecule closer to the origin. It helps with the curation >process and is easier for users of your entry as some software struggles with >such extreme transformations. Regards John From:

Re: [ccp4bb] PDBe Scientific Programmer / Bioinformatician

The deadline for applications to this post has been extended until the 22nd July 2018. Regards John From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of John Berrisford Sent: 21 May 2018 13:57 To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> Subj

[ccp4bb] reminder - PDBe Scientific Programmer / Bioinformatician

e data and sequence information from UniProt and other databases. For more details and to apply, please see the <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01168> listing on the EMBL careers site. Application deadline is 22nd April 2018 John -- John Berrisford P

[ccp4bb] reminder - PDBe Data Enrichment and Integration Coordinator

. For more details and to apply, please see the <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01116> listing on the EMBL careers site. Application deadline is 22nd April 2018 John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular B

[ccp4bb] PDBe Scientific Programmer / Bioinformatician

data and sequence information from UniProt and other databases. For more details and to apply, please see thelisting on the EMBL careers site. <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01168> Application deadline is 22nd April 2018 John -- John Berrisford PDBe European Bi

[ccp4bb] PDBe Data Enrichment and Integration Coordinator

. For more details and to apply, please see thelisting on the EMBL careers site. <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01116> Application deadline is 22nd April 2018 John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Labo

[ccp4bb] ORCIDs To Become Mandatory for OneDep Contact Authors

authors. At a later point, ORCID will be used to authenticate and reorganize access to deposition data within OneDep. Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Genome Campus Hinxton Cambridge CB10 1SD

Re: [ccp4bb] Parseable residue-ligand and/or residue-nucleic acid interaction database?

Dear Lucas You may want to look at credo http://marid.bioc.cam.ac.uk/credo We (PDBe) are working on integrating this into both our website and API. John PDBe -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Lucas Sent: 29 October 2018 13:53 To:

Re: [ccp4bb] Very strange LINK cards appearing in recent structures

Dear all We (the wwPDB) are actively looking into and correcting link records in the PDB. A lot of the recent re-releases were (and will continue to be) to correct links in existing PDB entries. I removed over 10,000 incorrect links in one sitting! We are also working to ensure that incorrect

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

2018. For more information on the position, please visit: <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01322> https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01322 Kind Regards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Mol

Re: [ccp4bb] Very strange LINK cards appearing in recent structures

important a determinant of the final structure as the observed data. phx On 12/11/2018 09:44, John Berrisford wrote: Dear all We (the wwPDB) are actively looking into and correcting link records in the PDB. A lot of the recent re-releases were (and will continue to be) to correct links i

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

Hi If you only want to view the EM volume for a PDB entry then you can do this directly from the PDB entry pages at PDBe. For example: http://pdbe.org/6a5p then click “3D visualisation” on the right hand side. It gets a compressed model and EM volume so will also work on your

Re: [ccp4bb] Search by name on the PDB fails

Dear Murpholino You can try the PDBe chem search http://pdbe.org/chem then use the second option on the form. You can change “=” to “like” to search for partial names. Regards John From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Murpholino Peligro Sent:

Re: [ccp4bb] clashscore question

Dear Xiaodi The wwPDB validation service does indeed add hydrogens using Reduce before calculating clashes. For more details of what processes are run when generating the wwPDB validation report see the on-line help

[ccp4bb] New PDB archive reference paper now in NAR 2019 Database issue

dictionary and major remediation efforts. The publication also emphasizes the importance of continued community interactions, the scientific and technical challenges the PDB faces, and charts the road ahead." -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecu

[ccp4bb] PDBe-KB ligand centric pages survey

, domains, ligand-binding sites and interfaces. In the next step we would like to present a similar aggregated view from a small molecule / ligand perspective. Thank you for your time, John Berrisford -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular

Re: [ccp4bb] PDBe-KB ligand centric pages survey

, Jon Agirre wrote: No link to the survey :( On Thu, 4 Apr 2019 at 15:55, John Berrisford wrote: Dear All, We are in the process of redesigning the ligand pages of PDBe and we would be grateful if you could fill out a short survey to help us understand what information about small molecules

[ccp4bb] The PDB Archive Reaches a Significant Milestone - 150,000 entries

www.wwpdb.org/news/news?year=2019#5c8c2db1ea7d0653b99c8774> The wwPDB -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http

Re: [ccp4bb] Java based structural database websites

I can second the recommendation of the Mol* project. Some of the data which is used for Olderado and Vivaldi is now part of the wwPDB validation report. This data is available from the PDBe API http://www.ebi.ac.uk/pdbe/api/doc/validation.html Additional data NMR validation data is

[ccp4bb] Mandatory mmCIF format for crystallographic depositions to the PDB

regarding these changes, please contact the wwPDB consortium via <mailto:deposit-h...@mail.wwpdb.org> deposit-h...@mail.wwpdb.org. The wwPDB consortium -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome

Re: [ccp4bb] ORCID being mandatory for PDB depositions

There are 3 lists of authors associated with a PDB deposition. 1. PDB entry authors - listed in audit_author in the public mmCIF / author record in the legacy PDB format 2. citation authors - listed in citation_author in the public mmCIF / JRNL record in the legacy PDB format 3. Contact

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

is 5th July 2019. For more information on the position, please visit: https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01435 Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus

[ccp4bb] wwPDB ligand validation updates

for the whole archive following the next archive-wide recalculation validation reports. For more information, please visit https://www.wwpdb.org/news/news?year=2019#5cfa7992ea7d0653b99c87d0 Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European

[ccp4bb] software developer position at PDBe

/searchjobs/index.php?ref=EBI01403 and the closing date is the 14th June 2019. Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529

[ccp4bb] Mandatory PDBx/mmCIF format for crystallographic PDB depositions

wwpdb.org <mailto:deposit-h...@mail.wwpdb.org> . Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pd

Re: [ccp4bb] “Bound ligand” versus “modified residue”

the file especially mmCIF. Maybe John Berrisford can comment. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov <ma

Re: [ccp4bb] “Bound ligand” versus “modified residue”

link as needed. Then obviously one must also describe the peptide links made by A01. Cheers -- Ian On Thu, 25 Apr 2019 at 09:48, John Berrisford mailto:j...@ebi.ac.uk> > wrote: Hi The wwPDB procedure on this is listed in the “modified amino acids and nucleotides” s

Re: [ccp4bb] ORCID

Dear Jie ORCiD is mandatory for all authors that we communicate with during deposition (contact authors). One of the reasons is to allow us ensure that we are able to associate contact authors with all of their depositions even when their email address changes. These contact details are

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

feedback if we should be stricter and require a (or more than one) specific metric (e.g. CC1/2) – please be aware that any required metric must be available from all merging/scaling software. Thanks John From: CCP4BB Sent: 22 July 2019 11:32 To: John Berrisford Cc: CCP4BB

Re: [ccp4bb] challenges in structural biology

Stating the crystallography is dead might be a bit premature, it is still king for depositions. In 2017 we had a large number of fragment screening experiments deposited. From: CCP4 bulletin board On Behalf Of Nukri Sanishvili Sent: 15 July 2019 23:09 To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Dear Daniel The issues you mentioned are highlighted in the wwPDB validation report http://www.ebi.ac.uk/pdbe/entry-files/6mo0_full_validation.pdf and global issues with the entry are highlighted in the validation sliders http://www.ebi.ac.uk/pdbe/entry/pdb/6MO0 The validation sliders

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

November 2019. For more information on the position, please visit: https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01532 Kind Regards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus

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

2019. For more information on the position, please visit: https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01532 Kind Regards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton

Re: [ccp4bb] TLS parameters

Dear Pavel and Eleanor TLS records in mmCIF are standardised, so parameters from all refinement packages should be consistent with each other. Regards John From: CCP4 bulletin board On Behalf Of Pavel Afonine Sent: 19 November 2019 23:00 To: CCP4BB@JISCMAIL.AC.UK Subject: Re:

Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb

Dear Steve Please can you communicate with the wwPDB curation team through the OneDep system and we can look into specific issues with your deposition. We report all issues back to the developers (CCP4/Refmac/Phenix/Buster and OneDep) and they have all been very quick at fixing any problems.

[ccp4bb] Improving carbohydrates in the PDB

transition period, where the legacy data item, _chem_comp.pdbx_synonyms, will be retained. John John Berrisford PDBe +44 1223 492529 (tel:+44%201223%20492529) European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD

Re: [ccp4bb] REMARK 280 in mmcif?

HI Ben In mmcif we use _exptl_crystal_grow.pdbx_details. See http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_exptl_crystal_grow.pdbx_details.html John On 26 Jan 2020, 18:02 +, benjamin bax , wrote: > > In PDB files you could put all information about protein delivery buffer,

[ccp4bb] PDBe-KB COVID-19 pages - Download service and similar proteins data added

to these pages, which in the future will also be incorporated into our standard PDBe-KB pages. To read more about these new developments, please visit www.ebi.ac.uk/pdbe/about/news/pdbe-kb-covid-19-v2 Kind Regards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI

Re: [ccp4bb] molecular graphics program accessibility

Dear Careina Have you tried MolStar https://molstar.org/viewer/ This is the on-line viewer for both PDBe and RCSB webpages. For example pdbe.org/1cbs/3d Regards John From: CCP4 bulletin board On Behalf Of careinaedgo...@yahoo.com Sent: 17 April 2020 15:44 To:

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

HI This is great news. Can you let us at the PDB know the DOI's for each dataset so that we can associate the raw images with the PDB entry. We will be able to then show links to the raw images from PDB entry pages so that everyone can find them. Many thanks John John Berrisford PDBe +44 1223

[ccp4bb] New PDBe-KB COVID-19 Macromolecular Structure Data Portal

/covid-19), which will bring together all relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. Kinds regards John John Berrisford PDBe +44 1223 492529 European

[ccp4bb] Test the new sequence and ligand components at PDBe

<https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/4ph9/bound/IBP> https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/4ph9/bound/IBP Links to provide feedback are available in the green section at the bottom of each page. Kind Regards, John -- John Berrisford PDBe European Bioinformatics Institu

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

Dear all The wwPDB OneDep system allows depositors to provide DOIs of raw diffraction images during deposition to the PDB and once again encourages depositors to provide a DOI for raw images when they have submitted. Out of the 9665 X-ray entries that were released in 2019 we have DOI's for

[ccp4bb] PDBe-KB COVID-19 pages: more download options and antibody annotations

with similar structures. For full details see our news release (pdbe.org/news). Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529

[ccp4bb] Scientific Data Curation positions at PDBe and EMDB/EMPIAR

<https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01622> https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01622 Kind Regards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Cam

[ccp4bb] PDBe API webinar series - starts September 15th 2020

that you wish to attend. For more details about the webinars and to register, please visit <https://www.ebi.ac.uk/pdbe/about/events/pdbe-api-webinar-series> https://www.ebi.ac.uk/pdbe/about/events/pdbe-api-webinar-series Kind Regards, John -- John Berrisford PDBe Eu

[ccp4bb] Software developer position at PDBe

for applications is 16th November 2020. For more information on the position, please visit: <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01714> https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01714 Kind regards, John -- John Berrisford PDBe European Bioinformatics Institute

[ccp4bb] New release of PDBe-KB aggregated views includes superimposition and batch file downloads

dded-pdbe-kb-aggregated-views> https://www.ebi.ac.uk/pdbe/about/news/superimposition-and-batch-downloads-ad ded-pdbe-kb-aggregated-views Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxt

[ccp4bb] Updated Validation Reports for Released PDB Structures

validation/validation-reports> available. Your feedback, comments, and questions are welcome at <mailto:validat...@mail.wwpdb.org> validat...@mail.wwpdb.org. Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellco

[ccp4bb] What's missing in visualising biological sequence or structure data?

-- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatab

[ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB

the wwPDB website or contact us at <mailto:deposit-h...@mail.wwpdb.org> deposit-h...@mail.wwpdb.org. Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1

[ccp4bb] Reminder: Scientific Data Curation positions at PDBe and EMDB/EMPIAR

EMPIAR: <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01622> https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01622 Kind regards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust G

[ccp4bb] Improved Carbohydrate Data at the PDB

/carbohydrate-remediation> wwPDB carbohydrate remediation website or contact us at <mailto:deposit-h...@mail.wwpdb.org> deposit-h...@mail.wwpdb.org. John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust G

[ccp4bb] PDBe API webinar materials now available online

and webinars at the <https://www.ebi.ac.uk/pdbe/training/tutorials> PDBe training pages. Kind regards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Te

[ccp4bb] Bioinformatician position at PDBe

on the position, please visit: <https://www.embl.org/jobs/position/EBI01851> https://www.embl.org/jobs/position/EBI01851 Kind regards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome

[ccp4bb] Bioinformatician position at PDBe - in collaboration with groups at UCL and Uni. of Washington

egards, John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/

[ccp4bb] Modifications to support for SHEET and ligand SITE records in June 2021

John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/protei

[ccp4bb] More than 1,000 SARS-CoV-2 Coronavirus Protein Structures Available

n access to structural biology research data. Regards John PDB -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.

[ccp4bb] Web developer position for AlphaFold DB at EMBL-EBI

information and to apply, visit: embl.org/jobs/position/EBI01901 John Berrisford -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <h

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

ctural biology * Latest advances * The next 50 years: future perspectives (part 1) * The next 50 years: future perspectives (part 2) Register for the conference at s.embl.org/pdb21-01 Deadlines: Registration: 29 Sep 2021 John -- John Berrisford PDBe European Bioinforma

[ccp4bb] PI name, email, and ORCiD ID will be publicly available in PDBx/mmCIF data files starting September 24 2021

, email address, and ORCiD in public PDBx/mmCIF files. Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529

[ccp4bb] Bioinformatician position at PDBe

obs/position/EBI01913> Kind regards, John Berrisford To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to m

[ccp4bb] Bioinformatician position at PDBe in collaboration with CCP4

bl.org/jobs/position/EBI01923 Kind regards, John Berrisford -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.o

[ccp4bb] Improved access to small molecule definitions and Archive Inventories at the PDB

to be updated for the time being; they will eventually be removed from the PDB archive. Users are encouraged to utilize these new inventory files. Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome

Re: [ccp4bb] renaming chains

vaheh.oganes...@astrazeneca.com - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory

Re: [ccp4bb] keyword for refmac to output coordinates in cif format

, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 49

[ccp4bb] PDBx/mmCIF data files to include PI information

will be captured within the OneDep system. The responsible depositor who creates the deposition should make entry PI(s) aware of the policy change to include PI name, email address, and ORCiD in public PDBx/mmCIF files. Regards John -- John Berrisford PDBe European Bioinformatics