Re: [ccp4bb] Script for Comparing Structurally-Similar Proteins

2014-05-06 Thread Deborah Harrus
://www.ncbi.nlm.nih.gov/pubmed/11807243 http://www.ncbi.nlm.nih.gov/pubmed/15572780 Cheers, Deborah. -- Deborah Harrus, PhD Nuclear Receptors and Epigenetics Centre de Biochimie Structurale CNRS UMR5048 / INSERM U1054 Montpellier, France - Mail original - De: "Jacob Keller"

Re: [ccp4bb] Seeking software for Dynapro 99 DLS

2014-08-03 Thread Deborah Harrus
ve it. Have a nice day, Deborah. -- Deborah Harrus, PhD Post-doctoral fellow Team 3-1 Nuclear Receptors and Epigenetics Centre de Biochimie Structurale CNRS UMR5048 / INSERM U1054 29 rue de Navacelles 34090 Montpellier, France Phone: 04 67 41 77 19 - Mail original - De: "Ho Le

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

2015-06-26 Thread Deborah Harrus
Dear Weifei, You might want to use SUPCOMB from the ATSAS suite. http://www.embl-hamburg.de/biosaxs/supcomb.html Cheers, Deborah.

[ccp4bb] Distributing PDBx/mmCIF-Formatted Assembly Files

2022-05-05 Thread Deborah Harrus
.g., PyMol, ChimeraX, etc.) supports instantiation of assemblies directly from atomic coordinate files (_struct_assembly related categories), for improved efficiency. For any further information please email i...@wwpdb.org. Kind rega

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

2022-06-20 Thread Deborah Harrus
17th July 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI02041 Kind Regards, Deborah -- --- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European

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

2022-07-04 Thread Deborah Harrus
opportunity! Kind Regards, Deborah -- --- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton

Re: [ccp4bb] wwPDB_Deposition errors

2022-07-18 Thread Deborah Harrus
ed by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- ------- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI

Re: [ccp4bb] Regarding Protein biological assembly

2022-07-18 Thread Deborah Harrus
the files and then convert them using MAXIT (you could make a simple script to run them in batches)? May I ask for which purpose do you need files in PDB format instead of mmCIF format? Kind regards, Deborah Harrus PDBe On 11/07/2022 05:30, Abhilasha Thakur wrote: Hello, I have a long

[ccp4bb] PDB entries with extended CCD or PDB IDs will be distributed in the PDBx/mmCIF format only

2022-09-07 Thread Deborah Harrus
any further information please visit https://www.wwpdb.org/news/news?year=2022#630fee4cebdf34532a949c34 or contact us at i...@wwpdb.org. Kindest regards, Deborah Harrus -- --- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein

[ccp4bb] Improved EM validation with Q-score

2022-09-27 Thread Deborah Harrus
contact us at validat...@mail.wwpdb.org. Kindest regards, Deborah Harrus. -- --- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory

[ccp4bb] Bioinformatician position at PDBe

2022-10-06 Thread Deborah Harrus
PDBe data pipelines. The closing date for this post is 31st October 2022. For more information on the position, please visit: https://www.ebi.ac.uk/pdbe/about/jobs Kind regards, Deborah. -- --- Deborah Harrus, Ph.D. Lead

[ccp4bb] wwPDB Charter: Full and Associate Members

2022-10-14 Thread Deborah Harrus
/2021_wwPDB_Charter_with_Appendix.pdf). Kind regards, Deborah Harrus -- --- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus

[ccp4bb] AlphaFold DB models superposed on PDB structures at PDBe-KB

2022-10-20 Thread Deborah Harrus
‘3D view of superposed structures’. Read more at https://www.ebi.ac.uk/pdbe/news/compare-experimental-models-pdb-alphafold-models-pdbe-kb Kind Regards, *Deborah Harrus -- --- Deborah Harrus, Ph.D. Lead Annotator PDBe

[ccp4bb] Deprecation of FTP File Download Protocol in the PDB Archive

2022-11-03 Thread Deborah Harrus
HTTP/S traffic.  * rsync.wwpdb.org for RSYNC Starting September 2023, wwPDB will start enforcing use of these updated DNS names for the preparation of FTP protocol deprecation. Please contact i...@wwpdb.org with any questions. Kind regards, Deborah Harrus PDBe

[ccp4bb] PDB Reaches a New Milestone: 200,000+ Entries

2023-01-11 Thread Deborah Harrus
b.org/news/news?year=2023#639b9e337f8444f313d20414 Kind regards, Deborah Harrus -- ------- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology

[ccp4bb] Enhanced Collection of Starting Models

2023-02-01 Thread Deborah Harrus
applications. Read this news on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63d97981c031758bf1c30fec Kind regards, Deborah Harrus PDBe -- ------- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Eur

[ccp4bb] Structure Predictors: Use ModelCIF for Computed Structure Models

2023-02-01 Thread Deborah Harrus
PDBx/mmCIF data representation for computed structure models./bioRxiv/doi:10.1101/2022.12.06.518550 <https://doi.org/10.1101/2022.12.06.518550>. Read this news on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63d

[ccp4bb] wwPDB news: Prototype of PDB NextGen Archive now available

2023-02-07 Thread Deborah Harrus
aly: o pdb_8aly_xyz-enrich.cif.gz o pdb_8aly_xyz-no-atom-enrich.xml.gz Please contactinfo@wwpdb.orgwith any questions. Read this news on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826 Kind re

[ccp4bb] wwPDB news: Small Angle Scattering News

2023-02-14 Thread Deborah Harrus
on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63d97fafc031758bf1c30fed Kind regards, Deborah Harrus PDBe -- ------- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European Bioinformatics Institute (

[ccp4bb] wwPDB News: PDB entries with extended CCD or PDB IDs will be distributed in PDBx/mmCIF format only

2023-03-08 Thread Deborah Harrus
wPDB website: https://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7 Kind regards, Deborah. -- ------- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) Europe

[ccp4bb] wwPDB NEWS: Access Depositions Using ORCiD

2023-03-27 Thread Deborah Harrus
mandatory since 2018 <https://www.wwpdb.org/news/news?year=2018#5b2ced769ea23a2bf4a27b1d>. Read this news online: https://www.wwpdb.org/news/news?year=2023#641872ffe0a2cc03bf315460 Kind regards, Deborah Harrus PDBe -- -----------

[ccp4bb] wwPDB news: Prepare Depositions Using New pdb_extract Features

2023-05-12 Thread Deborah Harrus
ack XDS Xia2 Xscale Read this news online <http://www.wwpdb.org/news/news?year=2023#6455391c1d621d75127a7a46> Kind regards, Deborah. -- ------- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - P

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

2023-05-18 Thread Deborah Harrus
s.json.gz>orreleased_structures_last_modified_dates.json.gz <https://s3.rcsb.org/pub/pdb/holdings/released_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, De

[ccp4bb] New release of PISA-lite software for calculating macromolecular interaction data

2023-05-26 Thread Deborah Harrus
-interactions-data-pisa-lite <https://www.ebi.ac.uk/pdbe/news/improved-macromolecular-interactions-data-pisa-lite> Kind Regards, *Deborah Harrus PDBe -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - P

[ccp4bb] wwPDB News Update: ls-lR index file in the PDB archive to be removed on July 12, 2023

2023-06-05 Thread Deborah Harrus
on.gz> or released_structures_last_modified_dates.json.gz <https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz> in /pub/pdb/holdings/. Please contact i...@wwpdb.org with any questions. Kind regards, Deborah Harrus PDBe -- -----

[ccp4bb] wwPDB NEWS: DNS name changes for PDB archive downloads from wwPDB to start September 2023

2023-06-09 Thread Deborah Harrus
pdb.org with any questions. Read this news online <http://www.wwpdb.org/news/news?year=2023#647631aa1d621d75127a7a54> Kind regards, Deborah Harrus PDBe -- ----------- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration L

[ccp4bb] wwPDB: NMR restraint remediation conforms to standard NMR-STAR and NEF format

2023-06-15 Thread Deborah Harrus
less weight during structure calculation. For any further information about NMR data remediation, please contact us at deposit-h...@mail.wwpdb.org. See wwPDB news at https://www.wwpdb.org/news/news?year=2023#64875a3cd78e004e766a967c. Kind re

[ccp4bb] wwPDB News: PDB NextGen Archive Now Provides Intra-molecular Connectivity

2023-07-07 Thread Deborah Harrus
rg/news/news?year=2023#649f0801d78e004e766a9680> 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

[ccp4bb] wwPDB News: Updated Annotation and Standardization of Peptide Residues

2023-07-31 Thread Deborah Harrus
line: https://www.wwpdb.org/news/news?year=2023#64bff95ed78e004e766a9687 Kind regards, Deborah Harrus -- ------- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformati

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

2023-08-01 Thread Deborah Harrus
: https://www.embl.org/jobs/position/EBI02149 Kind Regards Deborah Harrus -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI

Re: [ccp4bb] mmciif pdb file editor.

2023-08-31 Thread Deborah Harrus
mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- ------- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Ba

[ccp4bb] wwPDB NEWS: Announcing Kyle Morris as EMDB's New Team Leader

2023-10-03 Thread Deborah Harrus
archive for future cryo-EM technologies, including machine learning applications. Read this news online <https://www.wwpdb.org/news/news?year=2023#6513b759d78e004e766a96a3> Kind regards, Deborah Harrus, on behalf of

[ccp4bb] wwPDB News: Distribution of Electron Microscopy metadata in PDBx/mmCIF file format

2023-10-06 Thread Deborah Harrus
(UK): https://ftp.ebi.ac.uk/pub/databases/emdb/structures/ *  PDBj (Japan): https://files.pdbj.org/pub/emdb/structures/ Read this news online <http://www.wwpdb.org/news/news?year=2023#651c49e2d78e004e766a96a4> Kind regards, Deborah Harrus, on be

[ccp4bb] PDBe ligands API survey - please give us your feedback

2023-10-20 Thread Deborah Harrus
your workflows Completing this survey should take approximately 10 minutes of your time. *Survey Deadline: October 24th.* Your participation is greatly appreciated, and we look forward to creating an even better PDBe experience together. Thank you for your time and consideration. Kind regards,

[ccp4bb] AlphaFold Database introduces sequence-based search and structure cluster members

2023-10-27 Thread Deborah Harrus
news/updates-from-data-resources/alphafold-database-update-sequence-based-search/ Kind regards, Deborah Harrus PDBe -- ------- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Euro

[ccp4bb] wwPDB News: Backbone Annotation and Standardization of Peptide Residues is Now Live

2023-11-27 Thread Deborah Harrus
and is funded by BBSRC grant number BB/V018779/1. Kind regards, Deborah Harrus, on behalf of the wwPDB -- ------- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinforma

[ccp4bb] wwPDB News - PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats

2023-12-13 Thread Deborah Harrus
gt;to assist with code revisions. To learn about PDBx/mmCIF, please visit https://mmcif.wwpdb.org/ <https://www.wwpdb.org/news/mmcif.wwpdb.org/>. For any further information please contact us at i...@wwpdb.org Kind regards, Deborah Harrus, on b

[ccp4bb] wwPDB News: Improved Depositor Experience Using ORCiD

2023-12-19 Thread Deborah Harrus
try ID * All columns now sortable While using a deposition ID and password to login into OneDep is still possible, we encourage depositors to use ORCiD for an improved user experience. Questions or feedback? contactdeposit-h...@mail.wwpdb.org. Kind regards, Deborah Harrus, on behalf of the

Re: [ccp4bb] "LINK" and "REMARK 290" of pdb file

2024-01-04 Thread Deborah Harrus
further assistance. Kind regards, Deborah Harrus PDBe On 29/12/2023 12:12, Qixu Cai wrote: Dear all, I'm working on the refinement of a crystal structure. In the structure, one crystal packing interface is mediated by a compound with two coordinate covalent bonds to two macromolecules

[ccp4bb] wwPDB News: Time-stamped Copies of PDB and EMDB Archives

2024-01-04 Thread Deborah Harrus
6cf> Kind regards, Deborah Harrus, on the behalf of wwPDB -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Mol

[ccp4bb] wwPDB News: Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

2024-01-10 Thread Deborah Harrus
<https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6>Five-character alphanumeric accession codes for CCD IDs are now issued by the OneDep system. For any further information please contact us ati...@wwpdb.org. Kin

[ccp4bb] wwPDB Preprint Published on NextGen Archive

2024-01-30 Thread Deborah Harrus
models. These PDBx/mmCIF files are directly compatible with various data visualization tools, simplifying the display of annotations on 3D structure views. Read this news online: https://www.wwpdb.org/news/news?year=2024#65b3f0e0c76ca3abcc925d12 Kind regards, Deborah Harrus, on b

[ccp4bb] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

2024-01-31 Thread Deborah Harrus
Be FTP area directly:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/ <https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/>* *Should you have any questions or require further assistance, please don't hesitate to contact us.* * Sincerely, Deborah

Re: [ccp4bb] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

2024-02-01 Thread Deborah Harrus
you yet harvesting and serving up the restraints used in refinement?  If not, that remains a huge gap, in my view.  (The chemists tend not to be aware that's even a thing, I keep discovering.) Frank On 31/01/2024 13:57, Deborah Harrus wrote: *Dear all,* *We're excited t

Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

2024-02-05 Thread Deborah Harrus
If it doesn't work, please feel free to send me your file and I will troubleshoot. Kind regards, Deborah Harrus PDBe On 30/01/2024 17:36, mdimarog wrote: Dear all, I am trying to deposit 2 structures to the PDBe, solved and refined in CCP4 (version 7), and checked in PRIVATEER as they hav

Re: [ccp4bb] Crystallizing a tough target

2024-02-05 Thread Deborah Harrus
To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- --------

[ccp4bb] wwPDB News: Latest Developments on the EMDB Published

2024-03-13 Thread Deborah Harrus
Research (2024) 52: D456–D465 https://doi.org/10.1093/nar/gkad1019 Kind regards, Deborah Harrus on behalf of the wwPDB -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe

[ccp4bb] wwPDB News: CryoEM Archiving and Validation Recommendations

2024-03-14 Thread Deborah Harrus
, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar (2024)/IUCrJ/11: 140–151https://doi.org/10.1107/S2052252524001246 Kind regards, Deborah Harrus on behalf of the wwPDB

[ccp4bb] New, free online AlphaFold training course

2024-03-14 Thread Deborah Harrus
Training platform: https://www.ebi.ac.uk/training/online/courses/alphafold/ If you have any questions about the course, please reach out to the EMBL-EBI training team on trainonl...@ebi.ac.uk. Kind regards, Deborah Harrus PDBe

[ccp4bb] wwPDB News: NMR Restraint Validation Paper Published

2024-03-22 Thread Deborah Harrus
. *Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank* Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, Yuhe Liang, Ezra Peisach, Irina Persikova, Theresa A Ramelot, Monica Sekharan, James Tolchard, John D

Re: [ccp4bb] Rescale merged data?

2024-04-19 Thread Deborah Harrus
required loops, and they now have advice on their website about this: https://staraniso.globalphasing.org/deposition_about.html. Randy -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank

Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread Deborah Harrus
Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for

Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread Deborah Harrus
. Diana Sent from my iPhone On Apr 26, 2024, at 8:04 AM, Deborah Harrus wrote:  Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 Kind regards, Deborah Harrus PDBe On 25/04/20

Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread Deborah Harrus
anything. Regards Garib On 26 Apr 2024, at 16:07, Deborah Harrus wrote: Hi Diana, Could you please clarify where you are searching? LIG is obsolete and definitely not in use. Cheers, Deborah On 26/04/2024 15:40, Diana Tomchick wrote: But I think that is a mistake, if you search for LIG in

[ccp4bb] Coming soon: Annotation of Protein Modifications in the PDB

2024-05-02 Thread Deborah Harrus
ear=2024#662fa1a565d8a8cacaf76f9c> Kind regards, Deborah Harrus, on behalf of the wwPDB -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute

Re: [ccp4bb] PDB validation - oligosacchides

2024-05-04 Thread Deborah Harrus
amp; conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) Europe

[ccp4bb] A favour to ask - EMBL-EBI user survey

2024-05-21 Thread Deborah Harrus
there are many demands on your time so I would like to thank you in advance for your participation and input. If you have any questions or comments about the survey please email co...@ebi.ac.uk. Kind regards, Deborah Harrus PDBe

Re: [ccp4bb] Topology diagram

2024-05-30 Thread Deborah Harrus
security/ -- --- 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.

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-06 Thread Deborah Harrus
Dear Jon, We will continue to serve the maps and are looking into updating the process to use the map coefficients now available in the wwPDB FTP data to make the maps compatible with the validation process. Kind regards, Deborah Harrus PDBe On 01/06/2024 14:28, Jon Cooper wrote: It

[ccp4bb] wwPDB: Announcing the New PDBx/mmCIF User Guide

2024-06-19 Thread Deborah Harrus
tps://mmcif.wwpdb.org/docs/user-guide/guide.html>) to share feedback on this guide by December 15, 2024. Your feedback will greatly contribute to future developments. Kind regards, Deborah Harrus, on behalf of the wwPDB -- ------- De

Re: [ccp4bb] Server to find structural similarity between nucleic acid structures

2024-06-24 Thread Deborah Harrus
- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- ------- Deborah Harrus,

Re: [ccp4bb] searching for ligands with double conformation

2024-06-24 Thread Deborah Harrus
?SUBED1=CCP4BB&A=1> -- ----------- 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

Re: [ccp4bb] Tools for identifying possible contaminants

2024-07-04 Thread Deborah Harrus
/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] PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)

2024-08-15 Thread Deborah Harrus
sed on community needs. In the near future, IHM data will also be available via wwPDB DOI landing pages and wwPDB partner websites. Questions or feedback? Contactdeposit-help@mail.wwpdb.orgorpdb-...@mail.wwpdb.org. Kind regards, Deborah Harrus, on behalf of the

[ccp4bb] Postdoctoral Opportunity in AI and Structural Biology (ARISE2 Fellowship)

2024-10-14 Thread Deborah Harrus
.org * -- --- 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 Hin

[ccp4bb] Annotation of Protein Modifications in the PDB

2024-10-09 Thread Deborah Harrus
>, and is funded by BBSRC grant number BB/V018779/1. Kind regards, Deborah Harrus, on behalf of the wwPDB -- ------- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European B

[ccp4bb] Access IHM structures at wwPDB DOI Landing Pages

2024-10-11 Thread Deborah Harrus
B IDs are mentioned. Users can distinguish IHM structures from PDB experimental structures on the DOI landing page where IHM structures have “integrative” as structure determination method displayed. Questions or feedback? Contactdeposit-help@mail.wwpdb.orgorpdb-...@mail.wwpdb.org. Deborah H

[ccp4bb] wwPDB Data Release Policy on Public Preprint Archives

2024-11-08 Thread Deborah Harrus
included with the deposition and manual review for PDB, EMDB, and BMRB IDs). Any concerns regarding this policy should be directed to the wwPDB leadership viadeposit-h...@mail.wwpdb.org. Kind regards, Deborah Harrus, on behalf of the wwPDB

[ccp4bb] Explore PDBe's Enhanced Ligand Pages with New Features

2024-11-27 Thread Deborah Harrus
d assistance, please feel free to reach out to us at pdbeh...@ebi.ac.uk <mailto:pdbeh...@ebi.ac.uk>. We hope you’ll find this new resource useful in your research! Kind regards, Deborah Harrus, on behalf of the PDBe team * -- -----

Re: [ccp4bb] Structure deposition problems with OneDep System

2025-01-31 Thread Deborah Harrus
ribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- ----------- Deborah Harrus, Ph.D. PD

[ccp4bb] wwPDB: Take the PDBx/mmCIF User Guide Survey and Win!

2025-01-31 Thread Deborah Harrus
ment. Your feedback is highly valued. Respondents can enter a drawing for a chance to win a prize from the wwPDB. The survey will remain open until February 28, 2025. Kind regards, Deborah Harrus, on behalf of the wwPDB -- ------- Deborah

[ccp4bb] PDB-Dev now PDB-IHM

2025-01-17 Thread Deborah Harrus
t;https://pdbj.org/>), will disseminate integrative structures on their respective websites. We look forward to supporting the structural biology community with depositing integrative structures toPDB-IHM <https://pdb-ihm.org/>. Questions or feedback? Contactdeposit-help@mail.wwpdb.o

[ccp4bb] Time-stamped Copies of PDB and EMDB Archives

2025-01-17 Thread Deborah Harrus
egards, Deborah Harrus, on behalf of the wwPDB -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Labo

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

2025-03-10 Thread Deborah Harrus
April 6, 2025. For more information on the position, please visit: https://embl.wd103.myworkdayjobs.com/en-US/EMBL/details/Scientific-Database-Curator_JR834 Kind Regards, Deborah Harrus PDBe To unsubscribe from the

[ccp4bb] wwPDB News: PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models

2025-03-11 Thread Deborah Harrus
es* <https://www.ebi.ac.uk/pride/markdownpage/crosslinking>. * Cross-reference PRIDE Crosslinking datasets in PDB-IHM depositions to enable robust validation. Read this news online: https://www.wwpdb.org/news/news?year=2025#67

Re: [ccp4bb] PDBe submission server maintenance...

2025-05-23 Thread Deborah Harrus
Dear Xavier, Our systems are currently under maintenance. Apologies for the inconvenience caused, and thanks for your patience. Kind regards, Deborah On 2025-05-23 12:41, Xavier Brazzolotto wrote: Since yesterday, the PDBe server seems to be in maintenance. Is there any issue? WE’LL BE BAC