://www.ncbi.nlm.nih.gov/pubmed/11807243
http://www.ncbi.nlm.nih.gov/pubmed/15572780
Cheers,
Deborah.
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Nuclear Receptors and Epigenetics
Centre de Biochimie Structurale CNRS UMR5048 / INSERM U1054
Montpellier, France
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De: Jacob Keller kell
it.
Have a nice day,
Deborah.
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Post-doctoral fellow
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Centre de Biochimie Structurale
CNRS UMR5048 / INSERM U1054
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Phone: 04 67 41 77 19
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De: Ho Leung Ng h
Dear Weifei,
You might want to use SUPCOMB from the ATSAS suite.
http://www.embl-hamburg.de/biosaxs/supcomb.html
Cheers,
Deborah.
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Kind regards,
Deborah Harrus
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the
archive for future cryo-EM technologies, including machine learning
applications.
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Completing this survey should take approximately 10 minutes of your time.
*Survey Deadline: October 24th.*
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opportunity!
Kind Regards,
Deborah
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Deborah
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European
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
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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.
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/.
For any further information please visit
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Deborah Harrus.
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‘3D view of
superposed structures’.
Read more at
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*Deborah Harrus
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/2021_wwPDB_Charter_with_Appendix.pdf).
Kind regards,
Deborah Harrus
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/news?year=2023#639b9e337f8444f313d20414
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Starting September 2023, wwPDB will start enforcing use of these updated
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wPDB website:
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Deborah.
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mandatory since 2018
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on the wwPDB website:
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Kind regards,
Deborah Harrus
PDBe
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o pdb_8aly_xyz-enrich.cif.gz
o pdb_8aly_xyz-no-atom-enrich.xml.gz
Please contactinfo@wwpdb.orgwith any questions.
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Kind regards,
De
ons.
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Kind regards,
Deborah Harrus
PDBe
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Lead Annotator
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Europ
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:
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less weight during structure calculation.
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us at deposit-h...@mail.wwpdb.org.
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Kind re
ws?year=2023#649f0801d78e004e766a9680>
Kind regards,
Deborah Harrus
PDBe
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PDBe Archive Project Leader, Biocuration Lead
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-interactions-data-pisa-lite
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Kind Regards,
*Deborah Harrus
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..@wwpdb.org with any questions.
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PDBe Archive Project Leader, Biocuration L
s.json.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
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:
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Kind Regards
Deborah Harrus
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PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI
line:
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Kind regards,
Deborah Harrus
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European Bioinformati
calepack
XDS
Xia2
Xscale
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Deborah.
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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/.
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nsubscribe from the CCP4BB list, click the following link:
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esn'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 have a lot
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
6cf>
Kind regards,
Deborah Harrus, on the behalf of wwPDB
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PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Mol
<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
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 from
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
and is
funded by BBSRC grant number BB/V018779/1.
Kind regards,
Deborah Harrus, on behalf of the wwPDB
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinforma
!
Are 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 to announce
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
P 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 Harrus
T
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 unkno
.
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 25/04/2024 16
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
with the
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
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
rity/
--
---
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
Cambr
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
, 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
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
.
*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
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
rity/
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---
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
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
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