Re: [ccp4bb] renaming chains

[John Berrisford]

Dear Vaheh

Usually we do not rename chains as part of the curation procedure.
There are instances when we do, for example when a chain has to be split 
into two chains and a new chain has to be defined, but this isn't 
typical.


Because of this the wwPDB mmCIF file for each entry will usually contain 
the chains as defined by the depositor.
If two letter chain IDs were used by the depositor then this is 
incompatible with the PDB format and a best effort PDB file is created. 
This will contain remapped chain IDs with a single letter for the 
chains.
If you are using this best effort PDB file then I would encourage using 
the mmCIF file instead.


If this is not the case, please can you share examples through our 
helpdesk (deposit-h...@mail.wwpdb.org) where this has occurred so we can 
investigate.


Many thanks

John

On 2021-11-01 15:00, Oganesyan, Vaheh wrote:

Hi All,

This question is mostly for RCSB and PDBe: why are you renaming chains
in the deposited PDB files? Why does it matter what letter is assigned
to the chain? For 1,2 or 3 chain structures it is manageable, but for
more chains and/or many complexes per asu this becomes quite a
challenge. And if chains are similar in shape it is a real pain.
Reading associated manuscripts and looking at those structures is an
additive that feels unnecessary.

Thank you in advance for explaining the logic behind.

Vaheh Oganesyan, Ph.D.

R | Biologics Engineering

One Medimmune Way, Gaithersburg, MD 20878

T:  301-398-5851

vaheh.oganes...@astrazeneca.com

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John Berrisford
PDBe
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European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
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Re: [ccp4bb] keyword for refmac to output coordinates in cif format

[John Berrisford]

Dear Mark

The keyword you want is

pdbout format mmcif

This is described here:
https://www.wwpdb.org/deposition/PDBxDeposit

Regards

John

On 2021-10-30 00:03, Mark J. van Raaij wrote:

Dear All,

this may be something simple but I can’t find it in the CCP4i GUI or 
online.

Is there a keyword to make refmac output the coordinates as a cif file
instead of a pdb file - or better, as both?
Or is it some other program that converts the formats?

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain



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[ccp4bb] Bioinformatician position at PDBe in collaboration with CCP4

[John Berrisford]

Dear Colleagues,

 

We have a bioinformatician position available in the PDBe team at the
European Bioinformatics Institute (EBI) on the Wellcome Genome Campus near
Cambridge.

 

We are looking for a structural bioinformatician who is interested in
developing methods for protein structure analysis to identify biologically
relevant conformational states and link these to macromolecular function.

 

The successful candidate will work in collaboration with Eugene Krissinel,
and the CCP4 core team at the Science and Technology Facilities Council, to
implement new data analysis methods, improve biological data processing
pipelines, perform data analysis, and contribute to developing user-facing
web pages.

 

The closing date for applications is 8th November 2021. For more information
on the position, please visit:

 

 <https://www.embl.org/jobs/position/EBI01923>
https://www.embl.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.org/> http://www.pdbe.org

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http://www.facebook.com/proteindatabank

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[ccp4bb] Bioinformatician position at PDBe

[John Berrisford]

Dear Colleagues,


We have an exciting opportunity for a bioinformatician interested in 
structural biological data and functional annotations to work within the 
Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics 
Institute (EMBL-EBI).



The work includes standardising post translational modification 
information within the PDB archive in collaboration with wwPDB partners, 
plus integration and display of post-translational and proteomics data 
on the PDBe and PDBe-KB web pages. This is a collaboration with the 
PRIDE data resource at EMBL-EBI and Juri Rappsibler 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 
<https://www.embl.org/jobs/position/EBI01913>



Kind regards,

John Berrisford




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

[John Berrisford]

Dear CCP4BB

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


wwPDB continues to support research, education, and drug discovery 
worldwide. Open access to PDB data has helped researchers in 
structure-guided discovery and development of anti-coronavirus drugs, 
vaccines and neutralizing antibodies. When researchers analyze existing 
PDB structures, such as working on a similar structure, they may often 
need additional information impossible to retrieve from the PDB entry 
file alone. In particular, it is not possible to obtain a point of 
contact in cases where there is no associated primary publication for an 
entry.


Following a recommendation from the IUCr Commission on Biological 
Macromolecules and the IUCr Committee on Data 
https://journals.iucr.org/a/issues/2020/06/00/es5023/index.html#SEC4.4, 
wwPDB will make public the PI name, email address, and ORCiD ID for 
initial PDB depositions or re-submissions made, starting September 24, 
2021. This will enable contact with the authors of every released PDB 
structure as of that date. This release will also align the PDB with the 
standard practices of providing corresponding author information by 
scientific journals


The dated acceptance of these PDB Terms and Conditions described above 
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 Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529



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

[John Berrisford]

Dear CCP4BB

Improved access to small molecule definitions
Individual Chemical Component Dictionary (CCD) and Biologically Interest 
molecule Reference Dictionary (BIRD) definitions are now accessible in a 
new FTP tree in the PDB archive. In response to user requests, these 
individual CCD and BIRD entry files can be found at 
/pdb/refdata/chem_comp/ and /pdb/refdata/bird/, respectively with last 
character hash as sub-directory.


For example:

/pdb/refdata/chem_comp/C/D8C/D8C.cif
/pdb/refdata/bird/prd/8/PRD_001068.cif
Improved access to information about PDB archive holdings
New inventory data files offer a quick overview of data in the archive. 
These files are in the extensible JSON format, and can be found under 
the new /pdb/holdings/ FTP tree.


The inventory lists provided include:

all_removed_entries.json.gz: list of removed PDB entries (obsolete, 
models) with entry authors, entry title, release date, obsolete date , 
and superseding PDB ID, if any.
current_file_holdings.json.gz: List of released PDB entries and file 
types present for each entry in the PDB Core Archive (e.g., coordinate 
data, experimental data, validation report, ...)
obsolete_structures_last_modified_dates.json.gz: List of obsolete PDB 
entries with last time of PDBx/mmCIF file modification
refdata_id_list.json.gz: List of released chemical reference entries, 
content types (e.g., Chemical Component, BIRD), and last time of 
reference file modification
released_structures_last_modified_dates.json.gz: List of released PDB 
entries with last time of PDBx/mmCIF file modification
unreleased_entries.json.gz: List of on-hold PDB entries, entry status, 
deposition date, and sequence pre-release information
The inventory (index) files historically provided in /pdb/derived_data/ 
will continue 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 Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529



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

[John Berrisford]

Dear CCP4BB

 

We are looking for a full-stack web developer interested in structural
biological data and predicted structures in the AlphaFold Protein Structure
Database (AlphaFold DB) to join the Velankar team at the European
Bioinformatics Institute (EMBL-EBI).

 

The successful candidate will work in a technical role as part of EMBL and
DeepMind's new partnership and will be responsible for data update, transfer
and processing, in addition to implementing API endpoints and developing
user-facing web pages.

 

The deadline for applications is 30th September 2021.

 

For more 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

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

Join the EMBL conference "Bringing Molecular Structure to Life: 50 Years of
PDB" and celebrate the 50th anniversary of The Protein Data Bank (PDB) with
us. With over 1 million unique users worldwide and more than 400 biomedical
data resources, the PDB represents the achievements and milestones of the
structural biology community.

 

The conference will be hosted virtually, running from 20th - 22nd October
2021. This timing coincides with the 50th anniversary of the original
announcement of the PDB archive, when the structural biology community
established the single worldwide archive for macromolecular structure data
in 1971.

 

The archive is managed by the Worldwide Protein Data Bank consortium (wwPDB)
which includes partner sites in Asia, Europe and America, making this a
truly global effort. The 50th anniversary is an opportunity to celebrate the
advances in structural biology and bioinformatics and peer into the future
prospects for these fields.

 

The session topics for the conference include:

*   Structural biology & applications in health and the environment
*   RNA/DNA molecular machines
*   The next 50 years: Genomics meets structural 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 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/proteindatabank>
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 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

wwPDB continues to support research, education, and drug discovery
worldwide. Open access to PDB data has helped researchers in
structure-guided discovery and development of anti-coronavirus drugs,
vaccines and neutralizing antibodies. When researchers analyze existing PDB
structures, such as working on a similar structure, they may often need
additional information impossible to retrieve from the PDB entry file alone.
In particular, it is not possible to obtain a point of contact in cases
where there is no associated primary publication for an entry.

 

Following a recommendation from the IUCr Commission on Biological
Macromolecules and the IUCr Committee on Data
(https://journals.iucr.org/a/issues/2020/06/00/es5023/index.html#SEC4.4),

wwPDB will make public the PI name, email address, and ORCiD ID for initial
PDB depositions or re-submissions made, starting September 24, 2021. This
will enable contact with the authors of every released PDB structure as of
that date. This release will also align the PDB with the standard practices
of providing corresponding author information by scientific journals

 

The dated acceptance of these PDB Terms and Conditions described above 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 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

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

[John Berrisford]

Dear Colleagues,

 

We are looking for a bioinformatician/scientific programmer to join the
Protein Data Bank in Europe (PDBe) team, working on a research project
exploring the utility of residue covariation data in predicting protein
quaternary structure. The project is a collaboration between PDBe, the
Orengo group at UCL and the Baker group at the University of Washington
(USA).

 

The post holder will identify the residue covariation data that can be
integrated into the PDBe-KB infrastructure and develop robust mechanisms for
data integration, visualisation and access. The post holder will have strong
software engineering skills and a background in bioinformatics.

 

The closing date for applications is 28th July 2021. For more information on
the position, please visit:

 <https://www.embl.org/jobs/position/EBI01864>
https://www.embl.org/jobs/position/EBI01864 

 

Kind 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.pdbe.org

 <http://www.facebook.com/proteindatabank>
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[ccp4bb] Bioinformatician position at PDBe

[John Berrisford]

Dear Colleagues,

 

We have a bioinformatician position available in the PDBe team at the
European Bioinformatics Institute (EBI) on the Wellcome Genome Campus near
Cambridge.

 

We are looking for a scientific programmer/bioinformatician with a strong
structural biology background and software engineering skills.

 

The successful candidate will create and improve biological data processing
pipelines, perform data analysis, and develop user-facing web pages for the
PDBe - Knowledge Base (PDBe-KB) resource.

 

The closing date for applications is 14th July 2021. For more information 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 Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

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

[John Berrisford]

Dear CCP4BB

 

 <http://www.wwpdb.org/news/news?year=2014#5764490799cccf749a90cde3> In
2014, PDBx/mmCIF became the PDB's archive format and the the legacy PDB file
format was frozen. In addition to PDBx/mmCIF files for all entries, wwPDB
produces PDB format-formatted files for entries that can be represented in
this legacy file format (e.g., entries with over 99,999 atoms or with
multi-character chain IDs are only available in PDBx/mmCIF)

As the size and complexity of PDB structures increases, additional
limitations of the legacy PDB format are becoming apparent and need to be
addressed.


Defining complex sheet records


Restrictions in the SHEET record fields in legacy the PDB file format do not
allow for the generation of complex beta sheet topology. Complex beta sheet
topologies include instances where beta strands are part of multiple beta
sheets and other cases where the definition of the strands within a beta
sheet cannot be presented in a linear description. For example, in PDB entry
5wln a large beta barrel structure is created from multiple copies of a
single protein; within the beta sheet forming the barrel are instances of a
single beta strand making contacts on one side with multiple other strands,
even from different chains.

This limitation, however, is not an issue in the PDBx/mmCIF formatted file,
where these complex beta sheet topology can be captured in _struct_sheet,
_struct_sheet_order, _struct_sheet_range, and _struct_sheet_hbond.

Starting June 8th 2021, legacy PDB format files will no longer be generated
for PDB entries where the SHEET topology cannot be generated. For these
structures, wwPDB will continue to provide secondary structure information
with helix and sheet information in the PDBx/mmCIF formatted file.


Deprecation of _struct_site (SITE) records


wwPDB regularly reviews the software used during OneDep biocuration. The
_struct_site and _struct_site_gen categories in PDBx/mmCIF (SITE records in
the legacy PDB file format) are generated by in-house software and based
purely upon distance calculations, and therefore may not reflect biological
functional sites.

Starting in June 2021, the in-house legacy software which produces
_struct_site and _struct_site_gen records will be retired and wwPDB will no
longer generate these categories for newly-deposited PDB entries. Existing
entries will be unaffected.

 

 

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

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http://www.facebook.com/proteindatabank

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

[John Berrisford]

Dear CCP4BB

 

With this week's update of the PDB, over one thousand (1018 to be exact!)
SARS-CoV-2-related structures are now freely available in the PDB.

The first SARS-CoV-2 structure, a high-resolution crystal structure of the
coronavirus main protease (PDB  <http://www.wwpdb.org/pdb?id=pdb_6lu7>
6lu7), was released early in the pandemic on February 5, 2020.

Since then, structural biologists have determined the structures of most of
the proteins in the SARS-CoV-2 proteome, including the spike protein binding
to its ACE2 receptor and neutralizing antibodies, and the main protease, the
papain-like proteinase, and other promising drug discovery targets. All of
the structures and related data are available for exploration from dedicated
pages on wwPDB partner websites:  <http://rcsb.org/covid19> RCSB PDB,
<https://www.ebi.ac.uk/pdbe/covid-19> PDBe,
<https://pdbj.org/featured/covid-19?tab=all> PDBj, and
<https://bmrb.io/coronavirus.shtml> BMRB.

Rapid public release of SARS-CoV-2 structures has greatly increased our
understanding of Covid-19, allowed direct visualization of emerging variants
of the virus, and facilitated structure-guided drug discovery and reuse to
combat infection. Open access to PDB structures has already enabled design
of effective vaccines against SARS-CoV-2.

The response of the research community to the pandemic has highlighted the
importance of open access to scientific data in real time. The wwPDB strives
to ensure that 3D biological structure data remain freely accessible for
all, while maintaining as comprehensive and accurate an archive as possible.

The impact of these over one thousand structures, and many more coronavirus
protein structures to come, stands as a testament to the importance of open
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.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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[ccp4bb] PDBe API webinar materials now available online

[John Berrisford]

Dear colleagues,

 

We have recently concluded our 6-part PDBe API webinar series and are
delighted to announce that all the videos and materials associated with the
series are now freely available online.

 

To access these materials, please visit
<https://pdbeurope.github.io/api-webinars>
https://pdbeurope.github.io/api-webinars. 

 

This webinar series covered PDBe's programmatic access options, from basic
data retrieval and search using the PDBe API to more advanced features,
including access and reuse of PDBe data visualisation components.

 

If you are a user of the PDBe API, then we encourage you to subscribe to our
PDBe API user mailing list, where we announce API releases, changes and
planned maintenance. To do so, please send an e-mail to
<mailto:pdbe-api-users-j...@ebi.ac.uk> pdbe-api-users-j...@ebi.ac.uk.

 

You can find all of PDBe's online tutorials 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

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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[ccp4bb] Software developer position at PDBe

[John Berrisford]

Dear CCP4BB,

 

We have a software developer position available in the PDBe team at the
European Bioinformatics Institute (EBI) on the Wellcome Genome Campus near
Cambridge.

 

We are looking for a software developer with a strong demonstrated record of
using Python programming language and a working knowledge of relational
and/or other database technologies to further develop and maintain the wwPDB
OneDep system.

 

The successful candidate will work closely with other members of the global
OneDep team to plan and implement improvements to the system.

 

The closing date 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 (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/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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[ccp4bb] Updated Validation Reports for Released PDB Structures

[John Berrisford]

Dear CCP4BB

 

All validation reports for released PDB entries have been updated and are
now available with recalculated percentiles. In addition, the validation
reports now include 2D diagrams highlighting ligand quality, map and model
fit for EM entries, and calculated map coefficients used for X-ray data
validation.

Updated validation reports for all X-ray, NMR, and 3DEM structures released
in the PDB archive are now available.

The updates include new percentile statistics reflecting the state of the
PDB archive on December 31, 2019 and calculated map coefficients used for
validation report generation.

The updated reports are accessible from the following FTP sites:

*  <ftp://ftp.wwpdb.org/pub/pdb/validation_reports/>
ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)

*  <ftp://ftp.rcsb.org/pub/pdb/validation_reports/>
ftp://ftp.rcsb.org/pub/pdb/validation_reports/ (RCSB PDB)

*  <ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/>
ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)

*  <ftp://ftp.pdbj.org/pub/pdb/validation_reports/>
ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj)

A snapshot of the previous version on June 10th is archived at
<ftp://snapshots.wwpdb.org/20200610/pub/pdb/> RCSB PDB and
<ftp://snapshots.pdbj.org/20200610/pub/pdb/> PDBj.

These updated wwPDB validation reports provide an assessment of structure
quality using widely accepted standards and criteria, recommended by
community experts serving in
<https://www.wwpdb.org/task/validation-task-forces> Validation Task Forces. 

In addition to recently introduced carbohydrate section and 2D Symbol
Nomenclature For Glycan (SNFG) images for oligosaccharides from
<https://www.wwpdb.org/documentation/carbohydrate-remediation> carbohydrate
remediation project, these reports now incorporate
<https://www.wwpdb.org/news/news?year=2019#5cfa7992ea7d0653b99c87d0>
visualization of ligand validation, model fit to electron density maps for
X-ray ligands. These include 2-dimensional diagrams of ligands, highlighting
geometric validation criteria and, for structures determined by
crystallography, 3-dimensional views of electron density. 

In addition,
<https://www.wwpdb.org/news/news?year=2019#5db841ceea7d0653b99c8839> EM map
analysis, and the fit of EM model to its map volume. FSC curves are also
included to compare reported and estimated resolution, where either half
maps or FSC data was uploaded.

Validation reports are provided to depositors through OneDep - the wwPDB
portal for validation, deposition and biocuration of structure data. The
wwPDB partners encourage the use of the  <http://validate.wwpdb.org/>
stand-alone validation server and the
<https://www.wwpdb.org/validation/onedep-validation-web-service-interface>
web service API at any time prior to data deposition. Depositors are
required to review and accept the reports as part of the data submission
process. Validation reports will continue to be developed and improved as we
receive recommendations from the expert Validation Task Forces (VTF) for
<https://www.wwpdb.org/task/xray> X-ray,  <https://www.wwpdb.org/task/nmr>
NMR,  <https://www.wwpdb.org/task/em> EM, and as we collect feedback from
depositors and users.

The wwPDB partners strongly encourage journal editors and referees to
request reports from authors as part of the manuscript submission and review
process, as already required by Nature, eLife, The Journal of Biological
Chemistry, the International Union of Crystallography (IUCr) journals, FEBS
journals, Journal of Immunology and Angew Chem Int Ed Engl. Reports are
date-stamped, display the wwPDB logo, and represent standardized wwPDB
validation. 

Further information and sample validation reports are
<https://www.wwpdb.org/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

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/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

Dear CCP4BB

 

Do you visualise biological sequence or structure data? 

What is missing for you in the current tools? 

The ELIXIR 3D-Bioinfo community
(https://elixir-europe.org/communities/3d-bioinfo) created a survey to find
out what your preferences and requirements are with respect to
visualisation. 

The Survey is available at https://forms.gle/Qtui4nx6xrivUcaG6, we would be
very grateful if you could complete it before the 31st of October.

The initial results from the survey will be presented at the online
3D-Bioinfo community meeting from 24-26/11/2020.

 

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.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

Dear CCP4BB

 

We are excited to be offering a 6-part PDBe API webinar series, introducing
different levels of programmatic access at PDBe, starting on the 15th
September.

 

This webinar series will range from basic data retrieval and search using
the PDBe API to more advanced features, including access and reuse of PDBe
data visualisation components.

The webinars are free to attend but the number of registrations are limited,
therefore it is recommended that you sign up in advance to avoid
disappointment. Each webinar has its own individual registration so please
sign up for all those 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

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/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

Dear CCP4BB

 

We have introduced some major changes to the
<https://www.ebi.ac.uk/pdbe/pdbe-kb/protein> PDBe-KB aggregated views of
proteins to allow easier in-depth analysis and comparison of protein
structures. These changes include comprehensive batch file download options,
superimposition and clustering of protein structures, and a raft of other
features previously only available through the
<https://www.ebi.ac.uk/pdbe/covid-19> PDBe-KB COVID-19 portal.

 

We have introduced a process that superimposes structures for a given
protein in the PDB based on their structural similarity. This enables users
of our PDBe-KB protein aggregated views to easily identify unique structural
conformations for each discrete section ("segment") of sequence for a given
UniProt entry. It also allows easy visualisation of all ligands that
interact with this segment of the protein. These structural clusters can be
easily displayed in your browser using the
<https://www.ebi.ac.uk/pdbe/about/news/introducing-mol-fast-interactive-3d-v
isualisation-your-browser-rcsb-pdb-and-pdbe> Mol* visualisation software. 

 

Also introduced in this update to the PDBe-KB aggregated views is a new
batch download service, allowing users to download all files for a specific
subset of entries. We have also integrated a number of features into the all
PDBe-KB aggregated views that were previously only available in the PDBe-KB
COVID-19 portal, including better handling of viral polyproteins, expanding
of the similar proteins section to the whole PDB, and highlighting of
interactions for molecules annotated as antibodies and PRDs (Peptide
Reference Dictionary).

 

To try these new features, visit any PDBe-KB aggregated views page - for
example, you can view the page for the COVID-19 main protease at
<https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins/PRO_449623>
https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins/PRO_449623.

 

For more information about these changes, please visit
<https://www.ebi.ac.uk/pdbe/about/news/superimposition-and-batch-downloads-a
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

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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[ccp4bb] Improved Carbohydrate Data at the PDB

[John Berrisford]

Dear CCP4BB

We have remediated and improved the representation of carbohydrates in the
PDB

As part of this remediation we have:

*   Standardized Chemical Component Dictionary nomenclature following
IUPAC-IUBMB recommendations
*   Standardized representation of oligosaccharides
*   Adopted glycoscience-community commonly used linear descriptors
using community tools
*   Annotated glycosylation sites in PDB structures

Detailed information about this project, including a list of remediated PDB
entries, is available at the
<https://www.wwpdb.org/documentation/carbohydrate-remediation> wwPDB
website. Developers of software packages that produce, access, or visualize
PDB data are encouraged to review this information and adapt their software
as soon as possible.

The wwPDB has created a new 'branched' entity representation for
polysaccharides, describing all the individual monosaccharide components of
these in the PDB entry. As part of this process, we have standardized atom
nomenclature of >1,000 monosaccharides in the Chemical Component Dictionary
(CCD) and applied a branched entity representation to oligosaccharides
(>8,000 PDB entries). To guarantee unambiguous chemical description of
oligosaccharides in the affected PDB entries, an explicit description of
covalent linkage information between their monosaccharide units is included.
In addition, wwPDB validation reports provide consistent representation for
these oligosaccharides and include 2D representations based on the Symbol
Nomenclature for Glycans (SNFG).

To support the remediation of carbohydrate representation, software tools
providing linear descriptors were developed in collaboration with the
glycoscience community to enable easy translation of PDB data to other
representations commonly used by glycobiologists. These include Condense
IUPAC from  <https://github.com/GLYCAM-Web/gmml> GMML at University of
Georgia,  <https://gitlab.com/glyconavi/pdb2glycan> WURCS from PDB2Glycan at
The Noguchi Institute, Japan, and
<http://www.glycosciences.de/tools/pdb2linucs/> LINUCS from pdb-care at
Germany.

wwPDB has also used this opportunity to improve the organization of chemical
synonyms in the CCD by introducing a new _pdbx_chem_comp_synonyms data
category. This will enable more comprehensive capture of alternative names
for small molecules in the PDB. To minimize disruption to users, the legacy
data item, _chem_comp.pdbx_synonyms, will be retained for a transition
period through 2021.

The carbohydrate remediation project is a wwPDB collaborative project
carried out principally by  <http://rcsb.org/> RCSB PDB at Rutgers, The
State University of New Jersey and is funded by NIGMS grant U01 CA221216 in
collaboration with  <https://www.ccrc.uga.edu/> Complex Carbohydrate
Research Center at the University of Georgia.

If you have any comments or queries regarding these changes, please visit
the  <https://www.wwpdb.org/documentation/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 Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

Dear CCP4BB

PDB data will shortly incorporate a new data representation for
carbohydrates in PDB entries and reference data that improves the
Findability and Interoperability of these molecules in macromolecular
structures. In order to remediate and improve the representation of
carbohydrates across the archive, the wwPDB has: 

*   standardized Chemical Component Dictionary nomenclature following
IUPAC-IUBMB recommendations
*   provided uniform representation for oligosaccharides
*   adopted Glycoscience-community commonly used linear descriptors
using community tools
*   annotated glycosylation sites in PDB structures 

Starting July 29, 2020, users will be able to access the improved data via
FTP or wwPDB partner websites. Detailed information about this project is
available at  <https://www.wwpdb.org/documentation/carbohydrate-remediation>
the wwPDB website; lists of impacted entries and chemical components will be
published on this page after data release.

The wwPDB has created a new 'branched' entity representation for
polysaccharides, describing all the individual monosaccharide components of
these in the PDB entry. As part of this process, we have standardized atom
nomenclature of >1,000 monosaccharides in the Chemical Component Dictionary
(CCD) and applied a branched entity representation to oligosaccharides for
>8000 PDB entries. To guarantee unambiguous chemical description of
oligosaccharides in the affected PDB entries, an explicit description of
covalent linkage information between their monosaccharide units is included.
In addition, wwPDB validation reports provide consistent representation for
these oligosaccharides and include 2D representations based on the Symbol
Nomenclature for Glycans (SNFG).

To support the remediation of carbohydrate representation, software tools
providing linear descriptors were developed in collaboration with the
glycoscience community to enable easy translation of PDB data to other
representations commonly used by glycobiologists. These include Condense
IUPAC from  <https://github.com/GLYCAM-Web/gmml> GMML at University of
Georgia,  <https://gitlab.com/glyconavi/pdb2glycan> WURCS from PDB2Glycan at
The Noguchi Institute, Japan, and
<http://www.glycosciences.de/tools/pdb2linucs/> LINUCS from pdb-care at
Germany. 

Furthermore, to ensure continued Findability of 118 common oligosaccharides
(e.g., sucrose, Lewis Y antigen), we have expanded the Biologically
Interesting molecule Reference Dictionary (
<https://www.wwpdb.org/data/bird> BIRD) that contains the covalent linkage
information and common synonyms for such molecules.

wwPDB has also used this opportunity to improve the organization of chemical
synonyms in the CCD by introducing a new _pdbx_chem_comp_synonyms data
category. This will enable more comprehensive capture of alternative names
for small molecules in the PDB. To minimize disruption to users, the legacy
data item, _chem_comp.pdbx_synonyms, will be retained for a transition
period through 2021.

The carbohydrate remediation project is a wwPDB collaborative project that
is carried out principally by  <https://www.rcsb.org/> RCSB PDB at Rutgers,
The State University of New Jersey and is funded by NIGMS grant U01 CA221216
in collaboration with  <https://www.ccrc.uga.edu/> Complex Carbohydrate
Research Center at the University of Georgia.

If you have any comments or queries regarding the changes to carbohydrate
representation, please visit
<https://www.wwpdb.org/documentation/carbohydrate-remediation> 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 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

Dear Colleagues

 

There are two curator positions available in the PDBe and EMDB/EMPIAR teams
at the European Bioinformatics Institute (EBI) on the Wellcome Genome Campus
near Cambridge.

 

We are looking to recruit an expert structural biologist to join the PDBe
curation team. The work involves annotating preliminary PDB and EMDB
submissions and extracting relevant biological information.

 

We are also looking for an expert cryo-electron microscopist to join the
EMDB/EMPIAR team. The work will involve biocuration of EMDB and EMPIAR
depositions and the integration of this data with other bioinformatics
resources.

 

The closing date for applications for both posts is 30th June 2020. For more
information on the positions, please visit:

 

PDBe:  <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01532>
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01532

 

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 Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

Dear CCP4BB

 

There are two curator positions available in the PDBe and EMDB/EMPIAR teams
at the European Bioinformatics Institute (EBI) on the Wellcome Genome Campus
near Cambridge.

 

We are looking to recruit an expert structural biologist to join the PDBe
curation team. The work involves annotating preliminary PDB and EMDB
submissions and extracting relevant biological information.

 

We are also looking for an expert cryo-electron microscopist to join the
EMDB/EMPIAR team. This work would involve biocuration activity in both EMDB
and EMPIAR archives and the integration of this data with other
bioinformatics resources.

 

The closing date for both posts is 30th June 2020. For more information on
the positions, please visit:

 

PDBe:  <https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01532>
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01532

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 Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

We recently announced the new PDBe-KB COVID-19 data portal
(pdbe.org/covid19), allowing users to easily access a wealth of structural
data from the SARS-CoV-2 virus. We have now added annotations on antibody
classifications and details of peptide inhibitor molecules to the
interactions section. In addition, we have also extended the bulk download
options to entries with specific ligands or macromolecular interactions.

 

The interactions section of the PDBe-KB protein aggregated views previously
only identified macromolecules based on Uniprot accession. We have now
extended this for the COVID-19 pages to include antibody chains so that
these interactions are highlighted.

 

We recently introduced a new bulk file download service to the PDBe-KB
COVID-19 pages, and have now extended this to allow download for subsets of
entries containing macromolecular complexes or entries 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

 

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

[John Berrisford]

Dear CCP4BB

 

We are delighted to offer two new components available for beta testing on
our PDBe entry pages: the ProtVista sequence component on the PDBe
macromolecules pages and the LigEnv component on the ligands and
environments pages.

 

The ProtVista sequence view component has replaced our previous sequence
viewer on the PDBe macromolecules pages to help users interactively view
sequence-related data alongside topology and 3D structure. This allows the
display of much more data than was possible through our previous sequence
viewer. Try the ProtVista component on our macromolecules page at
<https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/3bow/protein/3>
https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/3bow/protein/3.

 

The LigEnv component is a new, interactive component displaying views of
ligand binding sites and will replace the static LigPlot image on our
ligands and environments pages. The viewer displays atomic-level
interactions between ligands and macromolecular binding sites and interacts
with an adjacent Mol* 3D viewer, allowing you to easily highlight key
binding residues in the 3D structure. Try the new LigEnv component on our
ligands and environments page at
<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 Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

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

[John Berrisford]

Dear CCP4BB

 

We recently announced the new PDBe-KB COVID-19 data portal
(PDBe.org/covid19), allowing users to easily access a wealth of structural
data from the SARS-CoV-2 virus. We have now added more functionality to
these pages, allowing bulk download of all relevant PDB structures and
highlighting all the PDB entries with high sequence identity to SARS-CoV-2
proteins.

 

To support SARS-CoV-2 research efforts, we aim to provide as much relevant
structure data as possible through the PDBe-KB COVID-19 data portal. This
means that we are actively working on adding new functionality 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)

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/proteindatabank>
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Re: [ccp4bb] molecular graphics program accessibility

[John Berrisford]

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: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] molecular graphics program accessibility

 

Dear all,

I have to teach online this year. I usually ask students to view and study 
protein structures using SPDBV and pymol. Does anyone know if these programs 
would run on smart devices? Not all students have computers. Or are there any 
alternative viewing programs that run on smart devices? 

thank you, 

Careina

 

  _  

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

[John Berrisford]

An unprecedented number of scientific efforts are taking place worldwide
in order to help combat the new coronavirus epidemic (COVID-19). One of
the biggest challenges in this fast-moving situation is to share data
and findings in a coordinated way, in order to understand the disease
and to develop treatments and vaccines.

To support research efforts to understand more about the 2019-nCoV virus
and the structures of its proteins, we have created dedicated PDBe-KB
pages to highlight important structural features of released PDB
entries. These pages highlight the ligand binding sites and residues
involved in protein-protein interactions, to help researchers easily
identify common features from all the available structure data.

Over the coming weeks we will further expand the functionality of these
pages, in order to make more relevant structural biology data available
for researchers. We would also appreciate your feedback so that we can
learn what is most useful for users and how we can implement more functionality.

To view the PDBe-KB COVID-19 Data Portal, please visit PDBe.org/covid19

In addition to these pages, EMBL-EBI has set up the COVID-19 Portal
(https://www.ebi.ac.uk/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 Bioinformatics Institute (EMBL-EBI) European Molecular Biology
Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK
https://www.pdbe.org



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

[John Berrisford]

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 492529 (tel:+44%201223%20492529)
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology 
Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK 
(https://maps.google.com/?q=European%20Bioinformatics%20Institute%20(EMBL-EBI)%20European%20Molecular%20Biology%20Laboratory%20Wellcome%20Trust%20Genome%20Campus%20Hinxton%20Cambridge%20CB10%201SD%20UK)
https://www.pdbe.org

On Mar 27 2020, at 7:26 pm, Gerard Bricogne  wrote:
> Dear all, It is a pleasure to be able to end the (GMT) week by calling for a 
> huge round of applause for the Diamond team, who this afternoon started 
> uploading a large collection of sets of raw diffraction images (77 as we 
> write but the upload is still ongoing) for PDB entries that were released two 
> days ago. Special thanks to Graeme Winter who organised the upload to Zenodo. 
> The datasets are collectively accessible via the following link: 
> https://zenodo.org/search?page=1=20=keywords:%22SARS-CoV-2%20main%20protease%22
>  Graeme asked that "major kudos [be given] to Zenodo developers who have been 
> very responsive with helping us do automated downloads". Happy scrutiny and 
> reprocessing of these datasets, and re-refinement of the associated 
> structures, to all hard-core MX addicts! With best wishes, Clemens & Gerard. 
> -- On Thu, Mar 19, 2020 at 10:00:11AM +, John Berrisford wrote: > Dear 
> all > > The wwPDB OneDep system allows depositors to provide DOIs of raw > 
> diffractio
 n 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 raw images in 205 of 
these entries. > > We would encourage depositors to provide the DOI for their 
raw images > when they are available. > > Regards > > John > > > On Mar 19 
2020, at 9:48 am, Joel Sussman wrote: > > > 19-Mar-2020 > > Dear Loes, Peter, 
Clemens & Gerard, > > I concur that it is crucial to preserve the original 
diffraction data > > and make it available to anyone who would like to use it. 
> > As an example, please see the very recent paper by > > Nachon et al (2020). 
"A second look at the crystal structures of > > Drosophila melanogaster 
acetylcholinesterase in complex with tacrine > > derivatives provides Insights 
concerning catalytic intermediates and > > the design of specific insecticides" 
Molecules 25 pii: E1198 > > [https://www.ncbi.nlm.nih.gov/pubme
 d/321558
91]. > > The study reexamines the original data, with modern software tools, > 
> the original data of a paper we published in 2000 (~20 years ago) and > > 
revealed features that had not been noticed. Specifically > > 1) previously 
unmodeled density in the native active site can be > > interpreted as stable 
acetylation of the catalytic serine. > > 2) Similarly, a strong density in the 
DmAChE/ZA complex, originally > > attributed to a sulfate ion, is better 
interpreted as a small molecule > > that is covalently bound. The complex is 
reminiscent of the > > carboxylate/BChE complexes observed in crystal 
structures of hBChE > > [Brazzolotto et al, 2012; Nicolet et al, 2003], and 
demonstrates the > > remarkable ability of ChEs to stabilize covalent complexes 
with carboxylates. > > Thus, the study demonstrates that updated processing of 
older > > diffraction images, and the re-refinement of older diffraction data, 
> > can produce valuable information that could not be detected in th
 e > > or
iginal analysis, and strongly supports the preservation of the > > diffraction 
images in public data banks. > > Best regards > > Joel > > 

 > > Prof. Joel L. Sussman. joel.suss...@weizmann.ac.il 
www.weizmann.ac.il/~joel > > Dept. of Structural Biology tel: +972 (8) 934 6309 
proteopedia.org > > Weizmann Institute of Science fax: +972 (8) 934 6312 > > 
Rehovot 76100 ISRAEL mob: +972 (50) 510 9600 > > 
-
 > > > > > >> On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes) > >> 
wrote: > >> > >> Dear Gerard, > >> > >> This is a great idea. Of course I am 
very much in favour of making > >> available r

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

[John Berrisford]

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 raw images in 205 of these entries.  

We would encourage depositors to provide the DOI for their raw images
when they are available.  

Regards

John


On Mar 19 2020, at 9:48 am, Joel Sussman  wrote:

> 19-Mar-2020
> Dear Loes, Peter, Clemens & Gerard,
> I concur that it is crucial to preserve the original diffraction data
> and make it available to anyone who would like to use it.
> As an example, please see the very recent paper by 
> Nachon et al (2020). "A second look at the crystal structures of
> Drosophila melanogaster acetylcholinesterase in complex with tacrine
> derivatives provides Insights concerning catalytic intermediates and
> the design of specific insecticides" Molecules 25 pii: E1198 
> [https://www.ncbi.nlm.nih.gov/pubmed/32155891].
> The study reexamines the original data, with modern software tools,
> the original data of a paper we published in 2000 (~20 years ago) and
> revealed features that had not been noticed. Specifically 
> 1) previously unmodeled density in the native active site can be
> interpreted as stable acetylation of the catalytic serine. 
> 2) Similarly, a strong density in the DmAChE/ZA complex, originally
> attributed to a sulfate ion, is better interpreted as a small molecule
> that is covalently bound. The complex is reminiscent of the
> carboxylate/BChE complexes observed in crystal structures of hBChE
> [Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the
> remarkable ability of ChEs to stabilize covalent complexes with carboxylates.
> Thus, the study demonstrates that updated processing of older
> diffraction images, and the re-refinement of older diffraction data,
> can produce valuable information that could not be detected in the
> original analysis, and strongly supports the preservation of the
> diffraction images in public data banks.
> Best regards
> Joel
> 
> Prof. Joel L. Sussman.        joel.suss...@weizmann.ac.il   
> www.weizmann.ac.il/~joel
> Dept. of Structural Biology   tel: +972  (8) 934 6309       proteopedia.org
> Weizmann Institute of Science fax: +972  (8) 934 6312
> Rehovot 76100 ISRAEL          mob: +972 (50) 510 9600
> -
>  
>  
>> On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes)
>>  wrote:
>>  
>> Dear Gerard,
>>  
>> This is a great idea. Of course I am very much in favour of making
>> available raw diffraction images, and such a virtual workshop could
>> demonstrate the usefulness of reprocessing raw diffraction data and
>> structural refinements. I am not at all afraid that archiving of raw
>> data that are the basis of a scientific paper will have significant
>> environmental effects: this is minor compared to our everyday use of
>> cloud services.  And as Graeme mentioned: when archiving raw data
>> make sure to add sufficient and correct meta data.
>>  
>> Best wishes,
>> Loes
>>  
>> ___
>> Dr. Loes Kroon-Batenburg
>> Dept. of Crystal and Structural Chemistry
>> Bijvoet Center for Biomolecular Research
>> Utrecht University
>> Padualaan 8, 3584 CH Utrecht
>> The Netherlands
>>  
>> E-mail : l.m.j.kroon-batenb...@uu.nl
>> phone  : +31-30-2532865
>> fax    : +31-30-2533940
>>  
>> Van: CCP4 bulletin board  namens Gerard
>> Bricogne 
>> Verzonden: woensdag 18 maart 2020 23:30
>> Aan: CCP4BB@JISCMAIL.AC.UK 
>> Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
>>  
>> Dear colleagues,
>>  
>> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
>> structures in the PDB seems to indicate that that there might be potential
>> to improve these if refinements could be repeated after some reprocessing
>> and further analysis of the raw diffraction images, rather than
>> against the
>> deposited merged data. This statement should in no way be construed
>> as a
>> criticism of the remarkable achievements of the research groups concerned,
>> who have been operating under tremendous time pressure, but as an exciting
>> opportunity to push methods to their limits on a uniquely significant class
>> of structures.
>>  
>> Another consideration is that the various logistical problems created by
>> COVID-19 may soon make it increasingly difficult to collect new diffraction
>> data on potential drug targets relevant to the fight against SARS-CoV-2,
>> underlining the importance of ensuring that the best results be obtained
>> from every dataset actually collected, and that the most useful conclusions
>> be drawn from the analysis of those datasets towards improving 

[ccp4bb] Improving carbohydrates in the PDB

[John Berrisford]

In July 2020, the wwPDB will roll out updated PDB structures and
reference data files with standardized representation of carbohydrate
molecules, improving the Findability and Interoperability of PDB data.
Detailed information about this work is available from the wwPDB website
(wwpdb.org/documentation/carbohydrate-remediation 
(https://link.getmailspring.com/link/03a8482f-0d25-4584-8cd5-d013814c9...@getmailspring.com/0?redirect=wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation=Y2NwNGJiQGppc2NtYWlsLmFjLnVr)),
 including PDBx/mmCIF
dictionary extensions and over 500 example files. We encourage
developers of software packages that produce, access, or visualize PDB
data to review this information and adapt their software.
Through collaboration with the glycoscience community, software tools
were developed to standardize atom nomenclature of nearly 800
monosaccharides in the Chemical Component Dictionary (CCD) and applied
branched polymeric representation to oligo- and polysaccharides within
the PDB archive, enabling easy translation to other representations
commonly used by glycobiologists. To guarantee unambiguous chemical
description of oligo-/polysaccharides in each of the nearly 12,000
affected PDB entries, we have included an explicit description of
covalent linkage information between their monomeric units. To ensure
continued Findability of common oligosaccharides (e.g., sucrose, Lewis X
factor), we have expanded the Biologically Interesting molecule
Reference Dictionary (BIRD, wwpdb.org/data/bird 
(https://link.getmailspring.com/link/03a8482f-0d25-4584-8cd5-d013814c9...@getmailspring.com/1?redirect=wwpdb.org%2Fdata%2Fbird=Y2NwNGJiQGppc2NtYWlsLmFjLnVr))
 which will contain the
covalent linkage information and common synonyms for such molecules.
wwPDB is also taking this opportunity to improve the organization of
chemical synonyms in the CCD by introducing a new
_pdbx_chem_comp_synonyms data category. This will enable more
comprehensive capture of alternative names for small molecules in the
PDB. To minimize disruption to users, there will be an initial
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 UK 
(https://link.getmailspring.com/link/03a8482f-0d25-4584-8cd5-d013814c9...@getmailspring.com/2?redirect=https%3A%2F%2Fmaps.google.com%2F%3Fq%3DEuropean%2520Bioinformatics%2520Institute%2520(EMBL-EBI)%2520European%2520Molecular%2520Biology%2520Laboratory%2520Wellcome%2520Trust%2520Genome%2520Campus%2520Hinxton%2520Cambridge%2520CB10%25201SD%2520UK=Y2NwNGJiQGppc2NtYWlsLmFjLnVr)
https://www.pdbe.org 
(https://link.getmailspring.com/link/03a8482f-0d25-4584-8cd5-d013814c9...@getmailspring.com/3?redirect=https%3A%2F%2Fwww.pdbe.org=Y2NwNGJiQGppc2NtYWlsLmFjLnVr)




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Re: [ccp4bb] REMARK 280 in mmcif?

[John Berrisford]

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, 
> crystallisation conditions and cryo conditions in
> REMARK 280
>
> (and pull it through in refmac with keyword
> pdbout copy remarks 280
> )
>
> Where are you meant to put all the information about what could be in your 
> crystal in mmcif_pdbx?
>
> Thanks, Ben
>
> Web (below) does not seem to give any very clear answers and I could not work 
> it out from looking at half a dozen recent pdb entries.
> Data item below is used in zero depositions. ..
>
>
> Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record
>                details about the components of the solutions that were 'mixed'
>                to produce the crystal.
>      
> http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/pdbx_exptl_crystal_grow_comp.html
>
> loop_
> _pdbx_exptl_crystal_grow_comp.crystal_id
> _pdbx_exptl_crystal_grow_comp.sol_id
> _pdbx_exptl_crystal_grow_comp.comp_id
> _pdbx_exptl_crystal_grow_comp.comp_name
> _pdbx_exptl_crystal_grow_comp.conc
> _pdbx_exptl_crystal_grow_comp.conc_range
> _pdbx_exptl_crystal_grow_comp.conc_units
> 4    'protein'     1  'protein'   25.    .  'mg/ml'
> 4    'protein'     2  'Tris HCl'  20.    .  'millimolar'
> 4    'protein'     3  'NaCl'       0.2   .  'molar'
> 4    'precipitant' 1  'PEG 4000'  12.5   .  'percent_weight_by_volume'
> 4    'precipitant' 2  'MES'        0.1   .  'molar'
> pdbout copy remarks 280
>
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Re: [ccp4bb] TLS parameters

[John Berrisford]

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: [ccp4bb] TLS parameters

 

Dear Eleanor,

 

Phenix reads and writes TLS records, both PDB and mmCIF format. It can also 
read (but not write) TLS records in REFMAC and BUSTER format.

 

In ATOM records Phenix outputs complete B factors, which includes both 
individual and TLS components (this is why they have ANISOU).

 

Phenix won't re-define (or define from scratch) TLS groups automatically unless 
it is asked to do so.

 

Pavel 

 

On Tue, Nov 19, 2019 at 7:36 AM Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk 
 > wrote:

And what about PHENIX?

E

 

On Tue, 19 Nov 2019 at 15:33, Pierre Rizkallah mailto:rizkall...@cardiff.ac.uk> > wrote:

I can vouch for TLS blocks being used by REFMAC and the PDB validation servers, 
after some frustration I had with a deposition recently:
Towards the end of a refinement, I renamed some chains, to make oligomers in 
the a.u. contiguous in real space. Validation told me the centre of gravity as 
declared in the header is not the same as that produced from the coordinates. I 
edited the input TLS file, but it still produced the same outcome. I eventually 
realised that REFMAC reads the TLS blocks from the input PDB after reading all 
the other input instructions for the refinement run. This happening last, it 
overrides the declarations in the input TLS definitions file. In order to get 
the coordinates and the definitions to match, I had to remove the TLS blocks, 
produced by an earlier run of REFMAC, from the pdb input file, so that the new 
definitions can be followed, and appropriate TLS blocks produced. REFMAC would 
use pre-existing TLS blocks if they are in the PDB file.

The mismatch notwithstanding, REFMAC still worked correctly, although the 
shifts from the group origins would have looked strange if one tries to analyse 
the TLS motions with TLSANL. I admit, I don't view them. Moral of the story is, 
be careful when you rename chains at the end of the refinement!

Pierre Rizkallah
***
Dr Pierre Rizkallah, Senior Lecturer Structural Biology 
Institute of Infection & Immunology, Sir Geraint Evans Building, 
School of Medicine, Heath Campus, Cardiff, CF14 4XN
email: rizkall...@cardiff.ac.uk  
phone: +44 29 2074 2248
http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre

-Original Message-
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Robbie Joosten
Sent: 19 November 2019 15:14
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] TLS parameters

Hi Eleanor,

The blocks are reliably recorded in PDB entries but in some cases the 
renumbering of residues was not pushed through to TLS groups. Certain 
selections cannot be captured in the PDB format, for instance the split in main 
chain and side chain that Refmac allows. Fortunately that feature is hardly 
used.
Parsing TLS records is not straightforward, particularly the sets from Buster 
suffered a lot from inconsistent manual editing in the early days of TLS 
refinement. PDB-REDO's extractor does a decent job in getting selections and 
changing those into Refmac format, but there are definitely cases that it 
cannot do. We also have a tool that does this for mmCIF files which is not 
written by me and (therefore) much more sophisticated in handling more 
complicated cases. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board   > On Behalf Of Eleanor 
> Dodson
> Sent: Tuesday, November 19, 2019 3:59 PM
> To: CCP4BB@JISCMAIL.AC.UK  
> Subject: [ccp4bb] TLS parameters
> 
> Does anyone know how reliably the different programs record and use 
> these blocks from the PDB file?
> 
> Eleanor
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> jiscmail.ac.uk  
> %2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1data
> =01%7C01%7Crizkallahp%40CARDIFF.AC.UK  
> %7Cf2a9834dd919481f28d508d76d030e
> 63%7Cbdb74b3095684856bdbf06759778fcbc%7C1sdata=BMwtQsLcQzHTeZcKqC
> Yg5W7MLDM7Phk0MUx8ohylApI%3Dreserved=0




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

[John Berrisford]

Hi

 

We are looking to recruit an expert structural biologist to join the PDBe
curation team on the Wellcome Genome Campus near Cambridge. The work
involves annotating preliminary PDB and EMDB submissions and extracting
relevant biological information. The closing date for the post is 29th
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

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

http://www.pdbe.org <http://www.pdbe.org/> 

http://www.facebook.com/proteindatabank

http://twitter.com/PDBeurope

 

 

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

[John Berrisford]

We are looking to recruit an expert structural biologist to join the PDBe
curation team on the Wellcome Genome Campus near Cambridge. The work
involves annotating preliminary PDB and EMDB submissions and extracting
relevant biological information. The closing date for the post is 29th
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

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

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. 

Please ensure that you are running the latest version of CCP4 as this
contains the latest updates which are required to ensure that deposition
goes smoothly. 

Hope this helps

John
PDBe

-Original Message-
From: CCP4 bulletin board  On Behalf Of
stephen.c...@rc-harwell.ac.uk
Sent: 25 September 2019 15:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Errors reading mmcif files when trying to deposit
coordinates to pdb

Dear Roberto,


I am using ccp4i at the moment, but am trying i2 to see if this corrects the
problem.  I have also tried pdb-extract as suggested by Isobel, but am still
awaiting the results.


Thanks fir the suggestions so far,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

From: Steiner, Roberto 
Sent: 25 September 2019 15:08:11
To: Carr, Stephen (MRC,RAL,RCAH)
Cc: ccp4bb
Subject: Re: [ccp4bb] Errors reading mmcif files when trying to deposit
coordinates to pdb

I assume you're using ccp4i and not i2. If you use the latter the mmcif
coords file produced should be ok.
I have had the same problem a few days ago.

Best wishes
Roberto


On 25 Sep 2019, at 15:00,
stephen.c...@rc-harwell.ac.uk
mailto:stephen.c...@rc-harwell.ac.uk>> wrote:

Dear ccp4ers,


I have refined several structures using refmac5 within ccp4i and tried to
upload the output mmcif files to the pdb in order to deposit the
coordinates/structure factors.

However, during the initial upload process when the files are scanned I get
the following errors:


ERROR - Read file 'input_file_1' failed:

syntax error at line 30421

ERROR - syntax error at line 30426

Warning - Duplicate category name chem_comp_atom at line 30428

Warning - Duplicate category name chem_comp_bond at line 30446

Warning - Duplicate category name chem_comp_angle at line 30467

ERROR - syntax error at line 30581

ERROR - syntax error at line 30585


These all lie after the coordinates in the dictionary part of the file.
When I have investigated this I cannot see any duplicated category names
that would result in the above warnings and the syntax errors are not a
result of anything obvious.  I have checked for hidden characters, found
none, and can see nothing else wrong.  Finally, line 30585 does not exist,
the file stops at 30584.


Has anyone had similar problems or any suggestions that might solve this?


Thanks,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

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oberto.steiner%40KCL.AC.UK%7C03ca2e3ed7d84887dd7f08d741c0deb8%7C8370cf1416f3
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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences
and Medicine King's College London

roberto.stei...@kcl.ac.uk
Phone 

Re: [ccp4bb] ORCID

[John Berrisford]

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 kept private and are not released into the PDB
archive.

 

ORCiD's are not required for authors who are just listed as entry or
citation authors. But we do encourage ORCiD's to be provided for these
authors if they are available. These author names, and any associated
ORCiD's, are made public upon PDB release. 

 

Please see

https://www.wwpdb.org/documentation/policy#toc_authorship

for further details of the different types of authors in a PDB entry. 

 

I hope this helps

 

Regards

 

John

 

From: CCP4 bulletin board  On Behalf Of Jie Liu
Sent: 19 August 2019 20:55
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ORCID

 

Dear all,


It's been a while since last time I deposited structures to PDB. Do I really
need an ORCID (Open Researcher and Contributor IDentifier) now to submit
files? Is it mandatory?

Thank you!
Jie

 

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

[John Berrisford]

Dear Harry

 

We will be shortly making it mandatory for depositors to provide a value for at 
least one of the merging statistics (Rmerge, Rpim, CC1/2 etc..). Most 
depositors do, but we want to ensure that all depositors do provide at least 
one value for a merging metric. 

 

We would welcome 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@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

Hi John

 

These are great, but the things that make me suspicious are the values of 
overall R(merge); these are tucked away in the full reports, rather than 
highlighted with all the other structural metrics in the validation sliders. It 
would be wonderful to be able to see at a glance where overall R(merge) values 
like these fit in with those of other deposited structures (even better if it 
could be drawn to the attention of authors before final deposition).

 

Kay and Gérard have already pointed out that the data processing here may have 
some issues.

 

Of course, those of us involved in teaching data processing have been 
emphasizing the importance of CC(1/2) rather than relying on R(merge) for 
yonks, but if CC(1/2) isn't given in the report it's all we have to go 

 

Harry

--

Dr Harry Powell


On 22 Jul 2019, at 10:05, John Berrisford mailto:j...@ebi.ac.uk> > wrote:

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 are shown on the entry pages at all wwPDB PDB sites 
(RCSB, PDBe and PDBj) and they all provide a link to download the wwPDB 
validation report directly from the entry page.

 

Regards

 

John

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Bonsor, Daniel
Sent: 19 July 2019 18:43
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

Would it be possible to add a public annotations section to the PDB, to allow 
us to potentially flag/warn whoever downloads that particular structure, there 
could be something wrong with it, such as wrong space group, no/poor density 
fitting for ligand. Something similar to PubPeer maybe? 

 

Daniel A. Bonsor PhD
Institute of Human Virology,
University of Maryland at Baltimore
725 W. Lombard Street N571
Baltimore
MD 21201

 


  _  


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Patrick Loll mailto:pjl...@gmail.com> >
Sent: Friday, July 19, 2019 1:17 PM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>  
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 

 

The idea of contacting the editor (and/or author) is an excellent one, and 
indeed the correct thing to do scientifically. However, I’m disillusioned: I’ve 
been down this path before with a high-profile vanity journal, and while the 
editors paid lip service to the notion that the record should be corrected, in 
reality they led me on for the better part of a year, and got me to write up 
detailed analyses of why the ligand positioning was not justified, before 
eventually saying “no, we don’t see any need to publish a correction.” I 
speculate that the journal prefers not avoid corrections, for fear that too 
many corrections will make the journal a less desirable destination.

> On 19 Jul 2019, at 11:23 AM, Bärbel Blaum  <mailto:baerbel.bl...@intherabio.com> > wrote:
> 
> Hi Rhys,
> the reported B-factors for the “ligands” are all way below the reported 
> B-factors for the protein chains, with the worst of the three complexes 
> reporting unitless numbers 23.2 and 64.8, respectively, just to highlight 
> *one* striking feature of the data collection and refinement table. So even 
> with the limited info normally available to reviewers this table should have 
> raised a red flag. After the re-refinement suggested by others, i.e. your own 
> proper assessment of the crystallographic data, if you do not find noteworthy 
> density you may want to contact the article’s editor with your results. If 
> you work in this field, i.e. really care about this paper scientifically and 
> you are not afraid to confront the authors you could suggest writing a 
> comment/direct response article but in my opinion that would only make sense 
> if you can be sure beforehand that it will be linked visibly to the actual 
> paper, else it will be a waste of time. And don’t forget that just because 
> one or so

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

[John Berrisford]

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 are shown on the entry pages at all wwPDB PDB sites
(RCSB, PDBe and PDBj) and they all provide a link to download the wwPDB
validation report directly from the entry page.

 

Regards

 

John

 

From: CCP4 bulletin board  On Behalf Of Bonsor,
Daniel
Sent: 19 July 2019 18:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

 

Would it be possible to add a public annotations section to the PDB, to
allow us to potentially flag/warn whoever downloads that particular
structure, there could be something wrong with it, such as wrong space
group, no/poor density fitting for ligand. Something similar to PubPeer
maybe? 

 

Daniel A. Bonsor PhD
Institute of Human Virology,
University of Maryland at Baltimore
725 W. Lombard Street N571
Baltimore
MD 21201

 

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > on behalf of Patrick Loll mailto:pjl...@gmail.com> >
Sent: Friday, July 19, 2019 1:17 PM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 

 

The idea of contacting the editor (and/or author) is an excellent one, and
indeed the correct thing to do scientifically. However, I’m disillusioned:
I’ve been down this path before with a high-profile vanity journal, and
while the editors paid lip service to the notion that the record should be
corrected, in reality they led me on for the better part of a year, and got
me to write up detailed analyses of why the ligand positioning was not
justified, before eventually saying “no, we don’t see any need to publish a
correction.” I speculate that the journal prefers not avoid corrections, for
fear that too many corrections will make the journal a less desirable
destination.

> On 19 Jul 2019, at 11:23 AM, Bärbel Blaum mailto:baerbel.bl...@intherabio.com> > wrote:
> 
> Hi Rhys,
> the reported B-factors for the “ligands” are all way below the reported
B-factors for the protein chains, with the worst of the three complexes
reporting unitless numbers 23.2 and 64.8, respectively, just to highlight
*one* striking feature of the data collection and refinement table. So even
with the limited info normally available to reviewers this table should have
raised a red flag. After the re-refinement suggested by others, i.e. your
own proper assessment of the crystallographic data, if you do not find
noteworthy density you may want to contact the article’s editor with your
results. If you work in this field, i.e. really care about this paper
scientifically and you are not afraid to confront the authors you could
suggest writing a comment/direct response article but in my opinion that
would only make sense if you can be sure beforehand that it will be linked
visibly to the actual paper, else it will be a waste of time. And don’t
forget that just because one or some of the authors did a bad job at the
crystallographic end other findings of the paper might still be solid – in
collaborations often one author is unable to critically evaluate another
author’s contribution and this would not be the first case were good
synthetic or biological work is presented along with a bad crystal
structure.
> By the way and a bit ironically this protein may have suffered bad
crystallography/scientific practice before - I think it was one of the fake
Krishna Murthy structures, right? The associated (now retracted) article I
mean is here
>
https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dih
ub 


 
 

 
 RETRACTED: Crystal structure of dengue virus NS3 protease in complex
with a bowman-birk inhibitor: implications for flaviviral polyprotein
processing and drug design - ScienceDirect - ScienceDirect.com | Science,
health and medical journals, full text articles and books.

www.sciencedirect.com  

COMMUNIC Crystal Structure of Dengue Complex with a Bowman-Bir ro L. 1Center
for Macromolecular C f A 8 U T MCLM 244, Birmingham AL 35294-0005, USA
2Department of Biochemistry and Molecular Biology, Kansas University Medical
Center 3901 Rainbow Boulevard Kansas City, KS 66160- 7421, USA Dengue
viruses are members of the Flaviviridae and cause dengue fever Dengue fever
and dengue hemorrhagic ...


> Kind regards, Bärbel
> ---
> Bärbel Blaum, PhD
> Inthera Bioscience AG
> Einsiedlerstrasse 34
> CH-8820 Waedenswil
> Switzerland
> E-Mail: baerbel.bl...@intherabio.com 

> Phone: +41 43 477 94 72--
>  
>  
>  
> 

Re: [ccp4bb] challenges in structural biology

[John Berrisford]

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
Subject: Re: [ccp4bb] challenges in structural biology

 

I know it is going to hijack the original topic but I could not help...

 

“The reports of death of (macromolecular) crystallography are greatly 
exaggerated.

If we believed the prognosticators, it has been dead since the 80s when some 
folks made the claim that the only relevant structures were those solved by NMR.

I think we've done quite well since then...

Best,

Nukri

 

On Mon, Jul 15, 2019 at 3:45 PM mailto:r...@mrc-lmb.cam.ac.uk> > wrote:

Hi Tassos, Tim,

I wonder why would you or anyone on this list worry whether biological
questions that can be asked and answered with structures are relevant to
justify the resources? I think there is abundant evidence that this is the
case. Unless your point is that crystallography is now dead for all practical
purposes... then yes, I fully agree :-) It would however be wrong to erase its
historical contribution to understanding biology.

Best wishes,

Radu


> I would wonder more if the biological questions you can *ask* with a (crystal)
> structure are sufficiently relevant to justify the resources.
>
> Sent from my iPhone
>
>> On 15 Jul 2019, at 22:08, Tim Grüne >  > wrote:
>>
>> Dear James,
>>
>> 10) are the biological questions that you can answer with a (crystal)
>> structure sufficiently relevant to justify the resources?
>>
>> Best,
>> Tim
>>
>>
>>
>> Am 15.07.2019 21:44, schrieb Holton, James M:
>>> Hello folks,
>>> I have the distinct honor of chairing the next Gordon Research
>>> Conference on Diffraction Methods in Structural Biology (July 26-31
>>> 2020).  This meeting will focus on the biggest challenges currently
>>> faced by structural biologists, and I mean actual real-world
>>> challenges.  As much as possible, these challenges will take the form of
>>> friendly competitions with defined parameters, data, a scoring system,
>>> and "winners", to be established along with other unpublished results
>>> only at the meeting, as is tradition at GRCs.
>>> But what are the principle challenges in biological structure
>>> determination today?  I of course have my own ideas, but I feel like I'm
>>> forgetting something.  Obvious choices are:
>>> 1) getting crystals to diffract better
>>> 2) building models into low-resolution maps (after failing at #1)
>>> 3) telling if a ligand is really there or not
>>> 4) the phase problem (dealing with weak signal, twinning and
>>> pseudotranslation)
>>> 5) what does "resolution" really mean?
>>> 6) why are macromolecular R factors so much higher than small-molecule
>>> ones?
>>> 7) what is the best way to process serial crystallography data?
>>> 8) how should one deal with non-isomorphism in multi-crystal methods?
>>> 9) what is the "structure" of something that won't sit still?
>>> What am I missing?  Is industry facing different problems than
>>> academics?  Are there specific challenges facing electron-based
>>> techniques?  If so, could the combined strength of all the world's
>>> methods developers solve them?  I'm interested in hearing the voice of
>>> this community.  On or off-list is fine.
>>> -James Holton
>>> MAD Scientist
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
>>>  =1
>>
>> --
>> --
>> Tim Gruene
>> Head of the Centre for X-ray Structure Analysis
>> Faculty of Chemistry
>> University of Vienna
>>
>> Phone: +43-1-4277-70202
>>
>> GPG Key ID = A46BEE1A
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
>>  =1
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
>  =1
>


-- 
Radu Aricescu
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44-(0)1223-267049
fax: +44-(0)1223-268305
www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu



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 =1

 

  

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

[John Berrisford]

>From today, July 1st 2019, submission of PDBx/mmCIF format files for
crystallographic depositions to the PDB is mandatory.

Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF
formatted files. For users of other structure determination/refinement
software packages, the wwPDB provides stand-alone and web-based tools to
convert legacy PDB format files into PDBx/mmCIF format: pdb_extract
<http://pdb-extract.wwpdb.org/>  and MAXIT
<http://sw-tools.rcsb.org/apps/MAXIT/index.html> . More information on
outputting and preparing PDBx/mmCIF format files for deposition can be found
on the wwPDB website
<https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files> .

For more information, view the full news release at the wwPDB website
<https://www.wwpdb.org/news/news?year=2019#5d17c1ceea7d0653b99c87e2>  or
contact the wwPDB on deposit-h...@mail.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.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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[ccp4bb] wwPDB ligand validation updates

[John Berrisford]

Hi

Our recent update to the wwPDB validation reports provides much clearer
validation information for ligands.

We now include 2-dimensional diagrams of ligands, highlighting geometric
validation criteria and, for structures determined by X-ray crystallography,
3-dimensional views of electron density.

We also provide calculated electron density map coefficients which were used
to generate the analysis in the validation reports.

Initially, the updated-style reports will be available to in deposition, and
publicly for newly released or updated PDB entries. The new features will be
available 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 Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

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

[John Berrisford]

Dear CCP4BB

 

We are looking to recruit an expert structural biologist to join the PDBe
curation team on the Wellcome Genome Campus near Cambridge. The work
involves annotating preliminary PDB and EMDB submissions and extracting
relevant biological information. The closing date for the post is 5th July
2019. For more information on the position, please visit:

 

https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01435

 

Regards

 

John

 

--

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PDBe

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European Molecular Biology Laboratory

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Hinxton

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[ccp4bb] software developer position at PDBe

[John Berrisford]

Dear CCP4BB

 

We are looking for a software developer with a strong demonstrated record of
using Python programming language and a working knowledge of relational
and/or other database technologies to further develop and maintain the
OneDep system.

 

The PDBe Team plays a leading role in developing OneDep - the common wwPDB
system for deposition, validation and biocuration of biomolecular structure
data - and this forms part of PDBe contribution to the wwPDB mission of
archiving high quality structure data.

 

The full description of the job is available at:

https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01403

 

and the closing date is the 14th June 2019.

 

Regards

 

John

--

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PDBe

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

[John Berrisford]

Hi Ian

 

Yes, I understand that this causes an issue. 

 

My suggestion is to take this off the CCP4BB list and initially discuss this 
amongst a smaller group as part of our protein modification remediation 
project. 

I will contact representatives of the major refinement programs (Refmac, 
Phenix, Buster) to start a discussion on the representation of modified amino 
acids. 

 

If anyone else would like to be involved in this discussion please contact me 
directly and I will add you do the discussion. 

 

Regards

 

John

 

From: Ian Tickle  
Sent: 25 April 2019 10:20
To: John Berrisford 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] “Bound ligand” versus “modified residue”

 

 

Hi John

 

As Pavel already mentioned, the problem with the ligand covalently bonded to a 
standard residue is that the bond is likely to change the geometry of the 
residue for atoms that are completely part of the residue, not just the atoms 
involved in the link.  In that case one would still need to give the (no 
longer) standard residue a different name (I use something like 'A01', 'A02' 
etc.) and copy most of the geometry from the standard entry, changing those 
near the covalent 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” section of 

https://www.wwpdb.org/documentation/procedure#toc_2

 

However, we are aware of the inconsistency in the PDB archive of how these 
modifications are represented and that there are lots of ligands which disagree 
with this procedure. 

 

We are in the early planning stages of a remediation of the PDB archive 
specifically on this topic and will be reaching out to the community to discuss 
this issue and to present our plans at a later date.

 

 

Regarding mmCIF representation

The mmCIF format allows both representations. 

 

In the case of a modified residue the residue has a parent of a standard 
residue and the one letter code of the standard residue. 

For example: phosphoserine, SEP, this ligand has a standard parent of SER and a 
one letter code of S. 

http://pdbe.org/chem/sep

So for example in PDB entry 1apm we have the following 

loop_

_entity_poly.entity_id 

_entity_poly.type 

_entity_poly.nstd_linkage 

_entity_poly.nstd_monomer 

_entity_poly.pdbx_seq_one_letter_code 

_entity_poly.pdbx_seq_one_letter_code_can 

_entity_poly.pdbx_strand_id 

_entity_poly.pdbx_target_identifier 

1 'polypeptide(L)' no yes 

;GNKKG(SEP)EQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDK

QKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFAEPHARFYAAQIVLTFEY

LHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTW(TPO)LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMA

AGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEA

PFIPKFKGPGDTSNFDDYIRV(SEP)INEKCGKEFTEF

;

;GNKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVV

KLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFAEPHARFYAAQIVLTFEYLHSL

DLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFA

DQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKG

PGDTSNFDDYIRVSINEKCGKEFTEF

 

Where we list both the one_letter_code which contains SEP and a canonical 
sequence which contains S. There is also TPO (phosphotheronine) in this example 
which has a canonical sequence of T.

 

(We are also aware that there are a number of modified residues which are 
missing the one letter code for the standard parent and are currently in the 
process of correcting this issue.)

 

In the other representation, where the modification is linked to a standard 
residue, the standard residue is listed in the sequence and the linkage between 
the standard residue and the modification is described in struct_conn. 

 

I hope this helps

 

John

 

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Nigel Moriarty
Sent: 24 April 2019 18:55
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: Re: [ccp4bb] “Bound ligand” versus “modified residue”

 

The "CYS with" means that the main chain is restrained and treated the same as 
"normal" CYS.

 

However, I'm not sure how the sequence should be handled in 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 <mailto:nwmoria...@lbl.gov> 
Fax   : 510-486-5909   Web  : CCI.LBL.gov <http://CCI.LBL.gov> 

 

 

On Wed, Apr 24, 2019 at 10:27 AM Pavel Afonine mailto:pafon...@gmail.com> > wrote:

Hi Ian,

perhaps there are 

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

[John Berrisford]

Hi

 

The wwPDB procedure on this is listed in the “modified amino acids and 
nucleotides” section of 

https://www.wwpdb.org/documentation/procedure#toc_2

 

However, we are aware of the inconsistency in the PDB archive of how these 
modifications are represented and that there are lots of ligands which disagree 
with this procedure. 

 

We are in the early planning stages of a remediation of the PDB archive 
specifically on this topic and will be reaching out to the community to discuss 
this issue and to present our plans at a later date.

 

 

Regarding mmCIF representation

The mmCIF format allows both representations. 

 

In the case of a modified residue the residue has a parent of a standard 
residue and the one letter code of the standard residue. 

For example: phosphoserine, SEP, this ligand has a standard parent of SER and a 
one letter code of S. 

http://pdbe.org/chem/sep

So for example in PDB entry 1apm we have the following 

loop_

_entity_poly.entity_id 

_entity_poly.type 

_entity_poly.nstd_linkage 

_entity_poly.nstd_monomer 

_entity_poly.pdbx_seq_one_letter_code 

_entity_poly.pdbx_seq_one_letter_code_can 

_entity_poly.pdbx_strand_id 

_entity_poly.pdbx_target_identifier 

1 'polypeptide(L)' no yes 

;GNKKG(SEP)EQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDK

QKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFAEPHARFYAAQIVLTFEY

LHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTW(TPO)LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMA

AGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEA

PFIPKFKGPGDTSNFDDYIRV(SEP)INEKCGKEFTEF

;

;GNKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVV

KLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFAEPHARFYAAQIVLTFEYLHSL

DLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFA

DQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKG

PGDTSNFDDYIRVSINEKCGKEFTEF

 

Where we list both the one_letter_code which contains SEP and a canonical 
sequence which contains S. There is also TPO (phosphotheronine) in this example 
which has a canonical sequence of T.

 

(We are also aware that there are a number of modified residues which are 
missing the one letter code for the standard parent and are currently in the 
process of correcting this issue.)

 

In the other representation, where the modification is linked to a standard 
residue, the standard residue is listed in the sequence and the linkage between 
the standard residue and the modification is described in struct_conn. 

 

I hope this helps

 

John

 

 

From: CCP4 bulletin board  On Behalf Of Nigel Moriarty
Sent: 24 April 2019 18:55
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] “Bound ligand” versus “modified residue”

 

The "CYS with" means that the main chain is restrained and treated the same as 
"normal" CYS.

 

However, I'm not sure how the sequence should be handled in 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 <mailto:nwmoria...@lbl.gov> 
Fax   : 510-486-5909   Web  : CCI.LBL.gov <http://CCI.LBL.gov> 

 

 

On Wed, Apr 24, 2019 at 10:27 AM Pavel Afonine mailto:pafon...@gmail.com> > wrote:

Hi Ian,

perhaps there are as many answers to this as many subscribers to this list, but 
personally "Cysteine with attachment" seems more logic and clear to me than 
calling the whole thing a different name. Although I would also understand 
arguments like if it is a CYS with an attachment it is not really CYS any more 
and perhaps should be called a unique name. From refinement viewpoint both a 
fine.

Pavel

 

On Wed, Apr 24, 2019 at 8:59 AM Ian Clifton mailto:ian.clif...@chem.ox.ac.uk> > wrote:

Hello everyone,

PDB structure 4qdu contains a “modified residue”, 30V. This is joined
into the rest of the main chain by means of LINK records. In 5kwj, a
similar type of modification is described as a cysteine with a
side‐chain LINK to its “bound ligand”, 6Y3 . (These structures are just
two clear examples we found to illustrate the question.)

Is there any reason to prefer one of these approaches over the other?
Does it just depend on what ligands are already in the PDB?

Thanks,
-- 
Ian Clifton ⚗ ℡: +44 1865 275677
Chemistry Research Laboratory ℻: +44 1865 285002
Oxford University : ian.clif...@chem.ox.ac.uk 
<mailto:ian.clif...@chem.ox.ac.uk> 
Mansfield Road   Oxford OX1 3TA   UK




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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[John Berrisford]

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 authors directly involved with the PDB deposition - with whom we 
communicate during deposition. Information collected about these authors is not 
made public. This information is stored internally within the wwPDB. 

ORCiD's are only required for the 3rd set and this information is not made 
public. We do provide the option of providing ORCiDs for groups 1 and 2, but it 
is not mandatory.

For more details please see the wwPDB policy on authorship:
https://www.wwpdb.org/documentation/policy#toc_authorship

For our privacy information please see
https://www.wwpdb.org/about/privacy

Both of these pages are linked from the OneDep deposition system. 


I hope this helps

Regards

John
PDBe

-Original Message-
From: CCP4 bulletin board  On Behalf Of V F
Sent: 09 April 2019 14:34
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ORCID being mandatory for PDB depositions

On 09/04/2019, Mark J van Raaij  wrote:
> Perhaps the poster is referring to the legality of creating an ORCID 
> on behalf of the collaborator?

Yes that is what I meant. (English not my first language)!

> That is how I interpreted it - but perhaps I over-interpreted...
>
> Another thing that came to my mind, not everyone has to be an author 
> of the PDB structure. Often all the authors of the corresponding paper 
> are also on the PDB entry, and there is nothing wrong with that, but 
> if a
> (non-crystallographer?) collaborator really doesn't want an ORCID, he 
> or she doesn't have to be an author of the PDB entry.
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology 
> Communications http://journals.iucr.org/f/
>
>
>> On 9 Apr 2019, at 14:20, Anastassis Perrakis  wrote:
>>
>> I am wondering, are there any arguments that would suggest that ORCID 
>> is not in line with GDPR requirements? You are disclosing your name 
>> etc to the PDB anyway, does it matter if its through ORCID or not?
>>
>> Tassos
>>
>>
>>> On Apr 9, 2019, at 14:04, V F  wrote:
>>>
>>> Dear all,
>>> Did anyone observe that oneDep from EBI made ORCID mandatory for 
>>> deposition? What am I supposed to do if my collaborators do not want 
>>> to create ORCID? (especially with GDPR I do not want to create 
>>> ORCID) Just posting here so that some one will respond? my mails are 
>>> going to /dev/null?
>>>
>>> Many thanks,
>>> VF
>>>
>>> 
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>> #
>> ###
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>
>
> ##
> ##
>
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Re: [ccp4bb] PDBe-KB ligand centric pages survey

[John Berrisford]

Hopefully you all have the link to the survey (below as plain text)
https://bit.ly/2FFmHFG

CCP4BB subscribers feedback was really helpful in designing the PDBe-KB 
protein pages. We are hoping for a similar response for help in designing 
the ligand pages.


Thanks

John


On 4 April 2019 16:12:19 Jon Agirre  wrote:
Thank you all for your help with this - it looks like John's link was being 
wiped out from the e-mail by an ad-blocking extension (?). So if you can't 
find the link, make sure you try deactivating whatever ad-blocker your 
browser is using :)



On Thu, 4 Apr 2019 at 15:56, 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 / ligands you would find useful. The 
survey is available at https://bit.ly/2FFmHFG




Recently, we have introduced protein-specific aggregated views on the 
structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in 
Europe Knowledge Base (PDBe-KB). We highlight the available information 
related to structures of specific proteins, including structural and 
functional annotations, 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 Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529



http://www.pdbe.org

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http://twitter.com/PDBeurope






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--

Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252

Twitter: @glycojones




--

Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252

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[ccp4bb] PDBe-KB ligand centric pages survey

[John Berrisford]

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 / ligands you would find useful. The
survey is available at https://bit.ly/2FFmHFG

 

Recently, we have introduced protein-specific aggregated views on the
structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in
Europe Knowledge Base (PDBe-KB). We highlight the available information
related to structures of specific proteins, including structural and
functional annotations, 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 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/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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Re: [ccp4bb] Java based structural database websites

[John Berrisford]

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 planned to be added to the wwPDB 
validation report later this year. 

 

This data will be displayed in Mol* on PDBe webpages when Mol* is incorporated 
into our web pages. 

 

John

 

From: CCP4 bulletin board  On Behalf Of Jose Duarte
Sent: 19 March 2019 18:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Java based structural database websites

 

Indeed java in the browser was killed a long time ago.

 

But the good news is that plenty of alternatives exist, written in native (to 
the browser) javascript. Wikipedia has a nice compilation of the different 
viewers, under the "Web-based systems" section:

 

https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems

 

I would particularly recommend the Mol* project:

 

https://molstar.org/

 

Jose

 

 

On Tue, 19 Mar 2019 at 10:37, Robbie Joosten mailto:robbie_joos...@hotmail.com> > wrote:

Hi Nick,

 

A bit of a hack I suppose, but you could use a (single use) VM with some old 
windows version that still works. 

E-mailing the developers directly is the way to go to figure out whether you 
can expect an update.

 

We had a similar problem with our own webserver (the Crystallographic Construct 
Designer ccd.rhpc.nki.nl  ) which was completely a java 
applet. The only real solution was a full rewrite. But that requires funding 
which  we luckily got from the West-Life project. 

Keeping websites online is is not easy with changing technology and getting 
funding is hard because it is not new science.

 

Cheers,

Robbie

 

 

 

On 19 Mar 2019 17:43, Nicholas Keep mailto:n.k...@mail.cryst.bbk.ac.uk> > wrote:

This is slightly off topic but I suspect people from PDBe etc read this 
bulletin board. 

Quite a number of very useful structural biology web sites (Olderado, 
Vivaldi, EMDB to name but a few) require java based viewers and hence no 
longer have full (or in the case of vivaldi any) functionality on up to 
date browsers. 

On a new computer it may prove hard or even impossible to find a browser 
that will work 

Are there plans to update these websites and is there any suggeted time 
scale? 

Any work rounds? 

Best wishes 

Nick 

-- 
Prof Nicholas H. Keep 
Executive Dean of School of Science 
Professor of Biomolecular Science 
Crystallography, Institute for Structural and Molecular Biology, 
Department of Biological Sciences 
Birkbeck,  University of London, 
Malet Street, 
Bloomsbury 
LONDON 
WC1E 7HX 

email n.k...@mail.cryst.bbk.ac.uk   
Telephone 020-7631-6852  (Room G54a Office) 
   020-7631-6800  (Department Office) 
Fax   020-7631-6803 
If you want to access me in person you have to come to the crystallography 
entrance 
and ring me or the department office from the internal phone by the door 

 

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 =1 

 

 

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

[John Berrisford]

With this week's update, the PDB archive has passed the milestone of 150,000
entries, and now contains a total of 150,145.

With this week's regular update, the PDB welcomes 262 new structures into
the archive. These structures join others vital to research and education in
fundamental biology, biomedicine, and bioenergy. Since its inception, the
size of the archive has increased tenfold roughly every 10-15 years: the PDB
reached 100 released entries in 1982, 1000 entries in 1993, and 10,000 in
the year 2000. Now that the 150,000th is made available, more than half of
the archive has been released in the past ten years.

The scientific community eagerly awaits the next 150,000 structures and the
invaluable knowledge these new data will bring. However, the increasing
number, size and complexity of biological data being deposited in the PDB
and the emergence of hybrid structure determination methods constitute major
challenges for the management and representation of structural data. wwPDB
will continue to work with the community to meet these challenges and ensure
that the archive maintains the highest possible standards of quality,
integrity, and consistency.

Development and future of the PDB archive and wwPDB organization is
described in the new reference publication for the PDB archive: Protein Data
Bank: the single global archive for 3D macromolecular structure data (
<https://doi.org/10.1093/nar/gky949> Nucleic Acids Res., 2019) and many
other papers, including Protein Data Bank (PDB): The Single Global
Macromolecular Structure Archive (
<http://dx.doi.org/%2010.1007/978-1-4939-7000-1> Methods in Molecular
Biology, 2017), How community has shaped the Protein Data Bank (
<http://dx.doi.org/10.1016/j.str.2013.07.010> Structure, 2013), and Creating
a Community Resource for Protein Science (
<http://onlinelibrary.wiley.com/doi/10.1002/pro.2154/abstract> Protein
Science, 2012).  <https://www.wwpdb.org/about/publications.php> A full list
is available.

For the full story see the wwPDB news release
<https://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://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

>From July 1st 2019 onward, mmCIF format files will become mandatory for
crystallographic depositions to the Protein Data Bank. PDB format files will
no longer be accepted for deposition of structures solved by these
techniques.

PDBx/mmCIF will be the only format accepted for deposition of PDB structures
resulting from macromolecular crystallography (MX), including X-ray,
neutron, fiber, and electron diffraction methods via OneDep starting July
1st 2019. The deposition of PDBx/mmCIF format files will improve the
efficiency of the deposition process and enhance validation through capture
of the more extensive experimental metadata supported by PDBx/mmCIF,
compared to the legacy PDB format.

For information about these changes, please visit the
<https://www.wwpdb.org/news/news?year=2019#5c6ad3c5ea7d0653b99c8766> wwPDB
news page. If you have any queries or comments 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 Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> http://www.pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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Re: [ccp4bb] clashscore question

[John Berrisford]

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

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#close_contacts

 

If you would like us to look into this in more detail please can you email us 
directly on 

validat...@mail.wwpdb.org  

with details of your validation session.

 

This email address is also listed on the wwPDB validation help page

https://www.wwpdb.org/validation/validation-reports

 

Regards

 

John

 

From: CCP4 bulletin board  On Behalf Of Sharan Karade
Sent: 16 January 2019 04:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] clashscore question

 

Dear Yu,

 

I think pdb validation server add hydrogen to the structure and then calculate 
the clashscore. The other methods you mentioned calculate clashscore without 
adding hydrogen to the structure.

 

Regards

Sharan

 

On Tue, Jan 15, 2019, 11:23 PM Xiaodi Yu mailto:uppsala@hotmail.com>  wrote:

Hi All:

 

I have a pdb file and the clashscores reported from both phenix and MolProbity 
were around 5, while the clashscore from the pdb validation server is 17. I 
wonder what may cause the difference? Any suggestion is appreciated.

 

Thank you.

 

Xiaodi 

 

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

[John Berrisford]

An important  <https://doi.org/10.1093/nar/gky949> new publication
describing the activities and development of the Protein Data Bank (PDB),
and authored by the whole wwPDB consortium, has been recently released in
the 2019 Database issue of Nucleic Acids Research.

Please see the following news release from the
<https://www.wwpdb.org/news/news?year=2018#5c05780d3675962a10fcf7a9> wwPDB
website:

" <https://doi.org/10.1093/nar/gky949> Protein Data Bank: the single global
archive for 3D macromolecular structure data has been published in the 2019
Database issue of Nucleic Acids Research. The paper was authored by "wwPDB
Consortium" to underscore the importance of the global wwPDB partnership in
managing the PDB archive.

This article describes the development of the PDB under the stewardship of
wwPDB, such as new archival content, master format and 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 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/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

We are looking to recruit an expert structural biologist to join the PDBe
curation team on the Wellcome Genome Campus near Cambridge. The work
involves annotating preliminary PDB and EMDB submissions and extracting
relevant biological information. The closing date for the post is 26th
December 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 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/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 




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

[John Berrisford]

Dear Frank

 

We are working together with the mmCIF working group on exactly this. 

mmCIF’s from phenix and refmac have parameters of the dictionaries used in 
refinement as additional data blocks. We are currently making sure that the 
output is identical from both packages so we can use it later. 

 

John

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von 
Delft
Sent: 12 November 2018 09:50
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Very strange LINK cards appearing in recent structures

 

Sorry, that was menat to be:  "... force us to deposit full details"

On 12/11/2018 09:49, Frank von Delft wrote:

While you're at it, can you force us full details of restraints used, whether 
it's the particular CCP4 library release, the CIF of the ligand, or the 
non-standard links?  

As far as I understand refinement, they're as least as 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 in existing PDB entries. I removed over 10,000 incorrect links
in one sitting!
 
We are also working to ensure that incorrect link records do not get added
into entries during annotation and part of this process is working with
developers of refinement packages to ensure that we receive links as they
were used in refinement in a standard format that we can read. 
 
As Robbie mentioned, if you do find any entries with incorrect link records
then do please let us know so we can correct them. 
 
Regards
 
John
PDBe
 
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Clemens Vonrhein
Sent: 12 November 2018 07:32
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: Re: [ccp4bb] Very strange LINK cards appearing in recent structures
 
Dear all,
 
we also have a lot of "fun" with LINK records when taking deposited PDB
structures into BUSTER refinement. Sometimes (but not often) there are
missing LINK records, but the vast number of problems is due to erroneous
LINK records added by annotation software it seems (based on a cut-off of
3.5A apparently).
 
Correcting those issues once reported is one option, but maybe revisiting
the idea about auto-generating LINK records during deposition would be
beneficial. At the end of refinement the various packages will have all
required and no wrong/additional LINK records in the final PDB file - and
deposition software should probably take those as-is without automatically
rewriting/adding/removing any (while still present a note/warning to
depositor about potentially missed LINK records according to annotation
software). This would most likely result in much fewer LINK problems in
deposited PDB structures.
 
As the format guide says:
 
  The LINK records specify connectivity between residues that is not
  implied by the primary structure. 
 
and specifically mentions bonds (not hydrogen bonds or salt-bridges):
https://www.wwpdb.org/documentation/file-format-content/format33/sect6.html# 
<https://www.wwpdb.org/documentation/file-format-content/format33/sect6.html> 
LINK
 
Cheers
 
Clemens
  
 
On Sun, Nov 11, 2018 at 07:31:55PM +, Robbie Joosten wrote:

Erroneous LINK records happen quite a lot and used to be the combination

of aggressive annotation software and depositors not paying attention to the
comments from the annotators. They make up a large fraction of the bug
reports I have sent to the PDB over the years. They are usually fixed very
quickly by the annotators, as long as someone takes time to report them.

This case looks like an error in a refinement program which nevertheless

should have been caught by the depositors. What I would like to know is
whether the deposited, pre-annotation model had the LINKs or not.

LINKs are a bloody nightmare when it comes to annotation. At the moment

there is no record keeping of targets and chemical modifications in a
dictionary on the side of the PDB so there is also no standardisation. IMO
mmCIF makes it easier to store the restraints with the coordinates, but
there is still no neat mapping by LINK identfiers the way the LINKR format
works in Refmac. I think that is a missed opportunity.

Sorry for the rant, I blame the F1.
 
Cheers,
Robbie
 
 
Op 11 nov. 2018 19:47 schreef Tristan Croll  <mailto:ti...@cam.ac.uk> 
:
 
I've seen instances like the following in roughly half a dozen 
deposited structures over the past year or so. Each time I've 
contacted the authors, who've been just as mystified as me by them - 
and certainly didn't add them on purpose. It seems to me that some 
fairly commonly-used package is erroneously turning clashes into LINK 
cards in some circumstances. I just found the following clearly wrong 
LINKs in 6caj (deposited January th

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

[John Berrisford]

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 link records do not get added
into entries during annotation and part of this process is working with
developers of refinement packages to ensure that we receive links as they
were used in refinement in a standard format that we can read. 

As Robbie mentioned, if you do find any entries with incorrect link records
then do please let us know so we can correct them. 

Regards

John
PDBe

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Clemens Vonrhein
Sent: 12 November 2018 07:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Very strange LINK cards appearing in recent structures

Dear all,

we also have a lot of "fun" with LINK records when taking deposited PDB
structures into BUSTER refinement. Sometimes (but not often) there are
missing LINK records, but the vast number of problems is due to erroneous
LINK records added by annotation software it seems (based on a cut-off of
3.5A apparently).

Correcting those issues once reported is one option, but maybe revisiting
the idea about auto-generating LINK records during deposition would be
beneficial. At the end of refinement the various packages will have all
required and no wrong/additional LINK records in the final PDB file - and
deposition software should probably take those as-is without automatically
rewriting/adding/removing any (while still present a note/warning to
depositor about potentially missed LINK records according to annotation
software). This would most likely result in much fewer LINK problems in
deposited PDB structures.

As the format guide says:

  The LINK records specify connectivity between residues that is not
  implied by the primary structure. 

and specifically mentions bonds (not hydrogen bonds or salt-bridges):
https://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#
LINK

Cheers

Clemens
  

On Sun, Nov 11, 2018 at 07:31:55PM +, Robbie Joosten wrote:
> Erroneous LINK records happen quite a lot and used to be the combination
of aggressive annotation software and depositors not paying attention to the
comments from the annotators. They make up a large fraction of the bug
reports I have sent to the PDB over the years. They are usually fixed very
quickly by the annotators, as long as someone takes time to report them.
> 
> This case looks like an error in a refinement program which nevertheless
should have been caught by the depositors. What I would like to know is
whether the deposited, pre-annotation model had the LINKs or not.
> 
> LINKs are a bloody nightmare when it comes to annotation. At the moment
there is no record keeping of targets and chemical modifications in a
dictionary on the side of the PDB so there is also no standardisation. IMO
mmCIF makes it easier to store the restraints with the coordinates, but
there is still no neat mapping by LINK identfiers the way the LINKR format
works in Refmac. I think that is a missed opportunity.
> 
> Sorry for the rant, I blame the F1.
> 
> Cheers,
> Robbie
> 
> 
> Op 11 nov. 2018 19:47 schreef Tristan Croll :
> 
> I've seen instances like the following in roughly half a dozen 
> deposited structures over the past year or so. Each time I've 
> contacted the authors, who've been just as mystified as me by them - 
> and certainly didn't add them on purpose. It seems to me that some 
> fairly commonly-used package is erroneously turning clashes into LINK 
> cards in some circumstances. I just found the following clearly wrong 
> LINKs in 6caj (deposited January this year):
> 
> LINK CD2 PHE I 266 CG2 THR I 272 1555   1555
>   1.47
> LINK CE2 PHE I 266 CG2 THR I 272 1555   1555
>   1.47
> 
> ... which looks like the attached image. The same bonds are also 
> specified in the mmCIF file, for the record.
> 
> Anyone have any clue?
> 
> Best regards,
> 
> Tristan
> 
> ##
> ##
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> ##
> ##
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



To 

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

[John Berrisford]

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: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Parseable residue-ligand and/or residue-nucleic acid 
interaction database?

Just so that we don't reinvent the wheel: is there any database or webservice 
on which one can parse the list of residue-ligand interactions for the entire 
PDB? I'd like to programmatically obtain information such as "in PDB 3hdl the 
Calcium 306 is in contact with
Asp223 or in PDB 5gjb Arg388 is in contact with the phosphate in the nucleic 
acid chain B". I know this information is available through pdbsum via 
ligplot/nucplot, but I'm unaware if it is possible to download the entire 
interaction database and if it is parseable.



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

[John Berrisford]

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 mobile phone…

 

John

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li
Sent: 10 September 2018 20:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for 
Cryo-EM structures.

 

Hi Kevin,

a)

If your goal is merely to display EM maps, then UCSF Chimera, COOT, pymol, etc. 
should all do. The EM maps are saved in the MRC format (.mrc or .mrcs). Despite 
a different extension and some minor differences in the headers, the MRC format 
is essentially the same format as our electron density maps (.ccp4 .map, etc.). 
Your favorite software for displaying crystallographic maps should work just 
fine. You will later find that owing to the fact that images are just 2D 
pixels, movies are series of 2D pixels,  maps are (saved as) 3D voxels, the 
single MRC/CCP4 format can hold many different types of data, including images, 
stacks of images, movies, maps, masks, etc..  That is why there is often also a 
.star file (similar to CIF files) that holds information on what is inside one 
or more MRC files. So be aware of what type of data you are opening. 

b)

To get an idea how cryo-EM single particle data processing works, the minimum 
you need would be RELION/EMAN2+UCSF Chimera (best for this job), which are all 
free to everyone. These will get you from the raw EM movies to the EM maps. 

If you have a computer with enough memory (16GB minimum, the more the better) 
and an Nvidia 1080TI card (~USD 800? a $150 1050TI can also get you started) 
you can already solve some EM structures! To do this, you need to get RELION 
and/or EMAN2 (ideally both):

https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Download_%26_install

http://blake.bcm.edu/emanwiki/EMAN2/Install

The reason for the 1080TI card is that it allows the programs to use its 300+ 
GPU cores to accelerate computations. This capability is provided by Nvidia's 
CUDA library. You need to download the CUDA 8.0 library from Nvidia. CUDA 8.0 
needs to be installed before you compile RELION if you are going to compile it 
yourself (not quite necessary). 

At present, EMAN2 only uses GPU at the particle picking step so it is not 
essential to have a GPU card just for running EMAN2. But classifications and 
refinements will be very slow (days and weeks) without a GPU.

Ideally you should install everything in Linux, such as Ubuntu 16.04 mate. You 
will also need softwares such as Motioncor2, GCTF, CTFFind, for some jobs in 
the workflow. Certain settings need to be put as environmental variables in the 
Linux system. Please figure them out yourself. It will take days to succeed for 
first-timers.

 

You can start playing by following the tutorials of either RELION or EMAN2 with 
their own tutorial datasets. These datasets are not really raw data though: 
they are particle "stacks" that contain the particles picked from the raw 
micrographs. But starting from there would be the easiest way to learn the 
essentials. BTW, following the EMAN2 tutorial does not involve using a GPU at 
all. This might be true for the non-GPU version of RELION too. 

 

If you want to start from the very beginning, you can download the 396GB 
proteasome movie dataset from EMPIAR:

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10025/

 

On youtube, Grant Jensen has a great series on cryoEM basics. I strongly 
suggest you to watch at least the part1, especially those having to do with 
CTF. 

https://www.youtube.com/watch?v=gDgFbAqdM_c 

 =PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8-

Zhijie





On 10/09/2018 1:01 PM, Kevin Jin wrote:

Dear Herman and all ccp4ers, 

 

Many thanks for the helps and education from all of you. 

 

I am a fresh beginner in Cryo-EM,  and have no access to those resource, like 
Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be valuable. 

 

Please forgive me for asking such a naive question.  I highly appreciate your 
comments and education.

 

Kevin

 

On Mon, Sep 10, 2018 at 5:28 AM mailto:herman.schreu...@sanofi.com> > wrote:

Hi Kevin, Pavel and others,

 

Since it seems that so far nobody answered the primary question: “Is there any 
sever available to create electron density maps for cryo-em structures?” So I 
will do it. The answer is very simple: They do not need to be created, they are 
available from the pdb!

 

To give an example: On the RCSB pdb web-site, I searched for entry 5vai. Then 
under the button “Download Files” I selected “Download EM Map” and downloaded 
emd_8653.map.gz. As the name suggests, this file needs to be unzipped, but this 
is trivial.

 

Then in Coot in the 

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

[John Berrisford]

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: 02 October 2018 06:18
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Search by name on the PDB fails

 

Hi all.

I was searching for ligands/molecules at 
www.rcsb.org/pdb/ligand/chemAdvSearch.do 
  (middle tab in blue). If I 
try to search with the third option, i.e. "name" of the ligand/molecule, it 
never works. I tried tetraethylene glycol, nitric oxide, cisplatin and even the 
example provided biotin. Fortunately specifying the identifier (i.e. 3 
letters..2 in some cases)... works. 

The problem is...what if I do not know the identifier?

 

I was wondering if you know another database that might work better for me? (or 
you, if your brain works better with chemical names instead of identifiers) 

 

 

Ps If there is some sort of coordinate file, preferably pdb or xyz, to download 
that will be better. 

 

 

* Pubchem works with sdf files which I do not like because if I open the sdf 
file for biotin with pymol and then save it as pdb, and then open this on coot 
it looks strange... (png attached)

(not sure if this is pymol's or coot's fault...but that's another thread I 
guess)

Thanks

 

 

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Re: [ccp4bb] PDBe Scientific Programmer / Bioinformatician

[John Berrisford]

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> 
Subject: [ccp4bb] PDBe Scientific Programmer / Bioinformatician

 

PDBe are looking for a Scientific Programmer / bioinformatician to work on
the wwPDB validation pipeline for structure data. 

The wwPDB validation pipeline is a critical component of OneDep data
deposition and biocuration system. The candidate will be involved in
implementing better validation metric for bound ligands as well as in
maintenance of the validation pipeline. 

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 22nd July 2018

John

 

 

--

John Berrisford

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European Molecular Biology Laboratory

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Tel: +44 1223 492529

 

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[ccp4bb] ORCIDs To Become Mandatory for OneDep Contact Authors

[John Berrisford]

The wwPDB OneDep system for deposition, validation and biocuration will
require contact authors to provide their unique ORCID identifiers
(https://orcid.org/) when preparing depositions later this summer. This
change will enable wwPDB efforts to correctly attribute PDB structures to
contact authors. At a later point, ORCID will be used to authenticate and
reorganize access to deposition data within OneDep.

 

Regards

 

John

 

--

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PDBe

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European Molecular Biology Laboratory

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 <https://www.pdbe.org/> https://www.pdbe.org

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Re: [ccp4bb] Regarding symmetry notion in coot

[John Berrisford]

>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: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 21 June 2018 17:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding symmetry notion in coot

 

 

On 20/06/18 20:49, Anurag Misra wrote:

 
What is the meaning of the last field — the one in curly brackets -- that 
describes the symmetry transformation of a given molecule in coot?


See Section 4.11 of Coot User Manual: "Symmetry"




 For example, for 
a given X Y Z, coot displays the symmetry transformation of an equivalent 
position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
 
Can the symmetry molecule be written like bellow by summing respective values?
 

 


In the general case, no. Move your molecule closer to the origin - so that the 
pre-translation is (0,0,0) - then coot will report "conventional" symmetry.

Regards,

Paul.

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
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 =1 




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[ccp4bb] Reminder - PDBe Scientific Programmer / Bioinformatician

[John Berrisford]

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 for a bioinformatician to work on the wwPDB validation
pipeline for structure data. 

The wwPDB validation pipeline is a critical component of OneDep data
deposition and biocuration system. The candidate will be involved in
implementing better validation metric for bound ligands as well as in
maintenance of the validation pipeline. The candidate will also be involved
in maintaining and developing the  <https://www.ebi.ac.uk/pdbe/docs/sifts>
SIFTS infrastructure. This is a critical component of bioinformatics
infrastructure that provides glue between PDB structure 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

 

--

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PDBe

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European Molecular Biology Laboratory

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

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[ccp4bb] Highlighting RNA in a protein world

[John Berrisford]

We may be called the Protein Data Bank in Europe (pdbe.org), but many PDB
entries also contain RNA, and we've just made finding them a lot easier. 

We've worked together with our colleagues at Rfam (http://rfam.xfam.org/) to
add their mappings of RNA molecules present in the PDB to our search 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

 

--

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PDBe

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European Molecular Biology Laboratory

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <https://www.pdbe.org/> https://www.pdbe.org

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[ccp4bb] Improvements to onedep deposition system

[John Berrisford]

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 is produced and it should be carefully reviewed, 
and any highlighted issues inspected. The report must be accepted by the 
depositor prior to re-submission of the data.


Any major data errors or data inconsistencies between the original and new 
files are displayed for review by the depositor so that these can be 
rectified prior to resubmission.


Overall, these changes should improve the quality of the data and the 
transparency of the file replacement process. If you have any questions or 
feedback regarding the new file replacement process then please log into 
your deposition session and contact us via the communication tab.




In addition, we are also making sure that we are open and clear about how 
we handle personal data in OneDep. We have updated the wwPDB privacy policy 
(http://www.wwpdb.org/about/privacy) to comply with the changes brought by 
the European Union data protection law (GDPR). If you have any questions 
about this privacy policy, please send them to deposit-h...@mail.wwpdb.org.



John

[ccp4bb] Exciting new updates at PDBe

[John Berrisford]

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 
the molecules in your search results.


See our news announcement for further details
https://www.ebi.ac.uk/pdbe/about/news/exciting-new-updates-pdbe

John

[ccp4bb] PDBe Scientific Programmer / Bioinformatician

[John Berrisford]

PDBe are looking for a bioinformatician to work on the wwPDB validation
pipeline for structure data. 

The wwPDB validation pipeline is a critical component of OneDep data
deposition and biocuration system. The candidate will be involved in
implementing better validation metric for bound ligands as well as in
maintenance of the validation pipeline. The candidate will also be involved
in maintaining and developing the  <https://www.ebi.ac.uk/pdbe/docs/sifts>
SIFTS infrastructure. This is a critical component of bioinformatics
infrastructure that provides glue between PDB structure 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 Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <https://www.pdbe.org/> https://www.pdbe.org

 <https://www.facebook.com/proteindatabank>
https://www.facebook.com/proteindatabank

 <https://twitter.com/PDBeurope> https://twitter.com/PDBeurope

 

[ccp4bb] reminder - PDBe Scientific Programmer / Bioinformatician

[John Berrisford]

PDBe are looking for a bioinformatician to work on the wwPDB validation 
pipeline for structure data. 

The wwPDB validation pipeline is a critical component of OneDep data deposition 
and biocuration system. The candidate will be involved in implementing better 
validation metric for bound ligands as well as in maintenance of the validation 
pipeline. The candidate will also be involved in maintaining and developing the 
 <https://www.ebi.ac.uk/pdbe/docs/sifts> SIFTS infrastructure. This is a 
critical component of bioinformatics infrastructure that provides glue between 
PDB structure 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
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529
 
https://www.pdbe.org
https://www.facebook.com/proteindatabank
https://twitter.com/PDBeurope

[ccp4bb] reminder - PDBe Data Enrichment and Integration Coordinator

[John Berrisford]

PDBe are looking to recruit a Data Enrichment and Integration Coordinator to 
help the PDBe team stay abreast of and meet the changing needs of the broad 
scientific community through enrichment, integration, and quality improvement 
of biomacromolecular structure data and tools for its delivery.

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 Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529
 
https://www.pdbe.org
https://www.facebook.com/proteindatabank
https://twitter.com/PDBeurope

[ccp4bb] PDBe Data Enrichment and Integration Coordinator

[John Berrisford]

PDBe are looking to recruit a Data Enrichment and Integration 
Coordinator to help the PDBe team stay abreast of and meet the changing 
needs of the broad scientific community through enrichment, integration, 
and quality improvement of biomacromolecular structure data and tools 
for its delivery.


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 Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

https://www.pdbe.org
https://www.facebook.com/proteindatabank
https://twitter.com/PDBeurope

[ccp4bb] PDBe Scientific Programmer / Bioinformatician

[John Berrisford]

PDBe are looking for a bioinformatician to work on the wwPDB validation 
pipeline for structure data.


The wwPDB validation pipeline is a critical component of OneDep data 
deposition and biocuration system. The candidate will be involved in 
implementing better validation metric for bound ligands as well as in 
maintenance of the validation pipeline. The candidate will also be 
involved in maintaining and developing theSIFTS infrastructure. 
<https://www.ebi.ac.uk/pdbe/docs/sifts>This is a critical component of 
bioinformatics infrastructure that provides glue between PDB structure 
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 Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

https://www.pdbe.org
https://www.facebook.com/proteindatabank
https://twitter.com/PDBeurope

[ccp4bb] Data Enrichment and Integration Coordinator at PDBe

[John Berrisford]

The Protein Data Bank in Europe team is looking to recruit a Data 
Enrichment and Integration Coordinator to help the PDBe team stay 
abreast of and meet the changing needs of the broad scientific community 
by developing pipelines for enrichment, integration, and quality 
improvement 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 Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

https://www.pdbe.org
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Re: [ccp4bb] LINK vs LINKR

[John Berrisford]

The deposition interface has the following instructions on the file 
upload page.



 Coordinate upload instructions

 * Coordinate files should be deposited in mmCIF format if possible.
 * Phenix and Refmac support direct output of mmCIF files (please
   seewww.wwpdb.org/deposition/PDBxDeposit
   <https://www.wwpdb.org/deposition/PDBxDeposit>for instructions).
 * If your refinement software does not export mmCIF files we encourage
   you to usepdb_extract <http://pdb-extract.wwpdb.org/>to prepare an
   mmCIF formatted file.
 * If you use a PDB formatted coordinate file, please check the PDB
   format requirements prior to file upload as deviation from these
   format requirements may result in data loss.
 * Seewww.wwpdb.org/documentation/file-formats-and-the-pdb
   <https://www.wwpdb.org/documentation/file-formats-and-the-pdb>


I hope this helps.

John
PDBe

On 10/12/2017 21:13, Bernhard Rupp wrote:


> and you can feed it your other relevant log files ((E.g. From XDS, 
Aimless, Phaser and you refinement program).


Provided the fossil remembers where those are….

Cheers,

BR

Sent from my Windows 10 phone



*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK 
<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Soisson, Stephen M 
<stephen_sois...@merck.com <mailto:stephen_sois...@merck.com>>

*Sent:* Sunday, December 10, 2017 9:58:09 PM
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* Re: [ccp4bb] LINK vs LINKR

Hey now, I resemble that remark ;)

Sent from my iPhone


On Dec 10, 2017, at 3:53 PM, Bernhard Rupp <hofkristall...@gmail.com 
<mailto:hofkristall...@gmail.com>> wrote:


or at least for the fossils still vi-ing PDB files…

Thx, BR

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey, USA 07033), and/or its affiliates Direct contact information
for affiliates is available at
http://www.merck.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 immediately by reply e-mail and then delete it from
your system.



--
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PDBe
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European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

http://www.pdbe.org
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Re: [ccp4bb] LINK vs LINKR

[John Berrisford]

Dear Eleanor

mmCIF does not have a equivalent of LINKR records.

If you define links during refinement then these are output as 
_struct_conn in mmCIF files. The _struct_conn records are used during 
deposition to determine if two atoms are linked, allowing using to 
validate chirality (such as ASN to a NAG) and ignore these atoms in 
clashes. Any _struct_conn records which are invalid due to one of the 
atoms missing will not affect the analysis at deposition, they will just 
be ignored.


Please try outputing an mmCIF file out of refmac and report any 
incorrect or missing _struct_conn records to the refmac developers.


John


On 10/12/2017 20:04, Eleanor Dodson wrote:
Dear John - sorry for my ignorance but does mmCIF provide a proper 
LINKR replacement?


Surely there is just as likely to be redundant LINK records as LINKR? 
It is easy enough to get rid of a residue 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 also present between unmodelled residues in
the PDB file (or were when we tested).

However, if you output an mmCIF file directly from refmac then the
link records are correctly written out into _struct_conn records
(mmCIF equivalent of LINK records) which are correctly handled by
the deposition system.

To do this simply add the keyword "pdbout format mmcif" to your
refmac commands and it will output an mmCIF file ready for
deposition.

I hope this helps

John

PDBe


On 09/12/2017 20:34, Bernhard Rupp wrote:


Dear Developers,

the TER issue in REFMAC seems to be fixed, but is really
necessary that REFMAC places LINKR

records instead of LINK records in the PDB header?

The PDB does not recognize those, and although it’s only a minor
nuisance to fix them in an editor,

one tends to forget this between revisions…or the PDB could
simply ignore the ‘R’….

Best, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org>

+1 925 209 7429 <tel:%28925%29%20209-7429>

+43 767 571 0536 <tel:+43%207675%20710536>

--

Many plausible ideas vanish

at the presence of thought

------



-- 
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 <tel:+44%201223%20492529>

http://www.pdbe.org
http://www.facebook.com/proteindatabank
<http://www.facebook.com/proteindatabank>
    http://twitter.com/PDBeurope




--
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] LINK vs LINKR

[John Berrisford]

Dear Bernhard

When we convert from PDB to mmCIF we do indeed ignore LINKR records as 
these are also present between unmodelled residues in the PDB file (or 
were when we tested).


However, if you output an mmCIF file directly from refmac then the link 
records are correctly written out into _struct_conn records (mmCIF 
equivalent of LINK records) which are correctly handled by the 
deposition system.


To do this simply add the keyword "pdbout format mmcif" to your refmac 
commands and it will output an mmCIF file ready for deposition.


I hope this helps

John

PDBe


On 09/12/2017 20:34, Bernhard Rupp wrote:


Dear Developers,

the TER issue in REFMAC seems to be fixed, but is really necessary 
that REFMAC places LINKR


records instead of LINK records in the PDB header?

The PDB does not recognize those, and although it’s only a minor 
nuisance to fix them in an editor,


one tends to forget this between revisions…or the PDB could simply 
ignore the ‘R’….


Best, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org>

+1 925 209 7429

+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 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] Removing a ter line present in the middle of the chain

[John Berrisford]

If you output an mmCIF file directly from refmac this avoids the TER 
record problem.


just add this

"pdbout format mmcif"

to your refmac command and it will output an mmCIF which can be used 
directly for deposition to the PDB


see https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files

Regards

John

PDBe

On 07/11/2017 15:02, Bernhard Rupp wrote:

This TER business is a common lament generally surfacing upon deposition.
PDB demands TER only after a peptide chain, but refmac inserts
them liberally after HETATM chains and in between them if the HET
monomers are not consecutively numbered.

Example:
.
HETATM 4626  C8  NAG A 652  -7.708  54.612  47.885  1.00 66.94   C
HETATM 4627  O7  NAG A 652  -6.870  54.052  45.727  1.00 74.93   O
TER4628  NAG A 652
HETATM 4629 CL   CL  A 801  21.660  57.665  44.396  1.00 72.44  CL
HETATM 4630 CL   CL  A 802   9.893  42.272  48.748  1.00 44.08  CL
TER4631  CL  A 802
ATOM   4632  N   PHE B  11  24.376 -12.877  29.777  1.00 80.09   N
ATOM   4633  CA  PHE B  11  24.701 -14.037  28.894  1.00 80.63   C
.
I have a crude hack removes aberrant TERs but it is
in F90 and no guarantees whatsoever case someone wants it.

Best, BR

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marcin 
Wojdyr
Sent: Tuesday, November 7, 2017 5:33 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Removing a ter line present in the middle of the chain

On 7 November 2017 at 12:28, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

Something (Refmac? Coot?? mystery?) was labelling all atoms in MSE
residues as HETATM and that was a BAD THING..

I don't dispute this, but that's what the 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: +44 1223 492529

http://www.pdbe.org
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[ccp4bb] A clearer 3D view of sugars

[John Berrisford]

Dear CCP4BB

Carbohydrates, even when formed from very few sugar units, can often be 
hard to interpret in three dimensions when all their atoms are shown. 
This week, PDBe have updated the 3D structure viewer (LiteMol) on our 
web pages to add a simpler representation of common pyranose sugars.


for example pdbe.org/5ezi

Approximately 10% of entries in the PDB archive contain some form of 
carbohydrate - that’s around 13.5 thousand PDB entries! We hope that 
adding this new feature will help users to see them more clearly.


See https://www.ebi.ac.uk/pdbe/about/news/clearer-3d-view-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
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[ccp4bb] EBI moving to HTTPS access

[John Berrisford]

Hi CCP4BB 

 

In December all access to EBI will be over HTTPS only. 

Users who visit the www.ebi.ac.uk <http://www.ebi.ac.uk>  web page over HTTP
will be seamlessly redirected to HTTPS.

However, we are aware that this redirect may cause issues for programmatic
access and you may find that 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

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

 <http://www.pdbe.org/> pdbe.org

 <http://www.facebook.com/proteindatabank>
http://www.facebook.com/proteindatabank

 <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

 

Re: [ccp4bb] PDB search help

[John Berrisford]

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 result you will need to compare “number_of_polymer_residues” and 
“max_observed_residues”. This will give you the observed ratio for each 
molecule (results are per molecule, not per PDB entry) in your result.

 

To make your query you can use our standard search page (pdbe.org) and with a 
small amount of reformatting use the same query in our search API. 

For example:

If you did a search on a main page the URL would look something like this:

https://www.ebi.ac.uk/pdbe/entry/search/index?text:hemoglobin 

 
_name:%22Neural%20hemoglobin%22_composition:%22protein%20structure%22_type:Protein

with all the search parameters encoded in the URL.

To use this in the API – take the part after the ? and change & to “ AND “ – 
the spaces are important here. 

i.e. 

text:hemoglobin_name:"Neural%20hemoglobin"_composition:"protein%20structure"_type:Protein

becomes

text:haemoglobin AND molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein

then append this to our search API URL 
(https://www.ebi.ac.uk/pdbe/search/pdb/select?q=)

https://www.ebi.ac.uk/pdbe/search/pdb/select?q=text:hemoglobin AND 
molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein

and then if you prefer JSON format to XML add =json to the end.  

https://www.ebi.ac.uk/pdbe/search/pdb/select?q=text:hemoglobin AND 
molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein=json

By default this will get you 10 result – to get more add =10 to the end 
and change 10 to a larger number. 

 

 

Hope this helps

 

John

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh
Sent: 27 September 2017 23:48
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB search help

 

Dear BB,

Sorry for the off topic. 

Does anyone know how to search the PDB for the entries that have the density 
only for part of the protein molecule rather than for the entire length of the 
protein attempted to crystallize?

 

 

Thanks,

Rajesh..

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

[John Berrisford]

Dear CCP4BB

The PDB is introducing versioning of PDB entries.
As part of this work a new FTP 
repository,ftp://ftp-versioned.wwpdb.org/now hosts versioned structural 
model files in PDBx/mmCIF and PDBML formats.
Asannounced 
<https://www.wwpdb.org/news/news?year=2017#5910c8d8d3b1d333029d4ea8>on 
May 17, 2017, wwPDB has introduced a versioning system to enable 
depositor-initiated or wwPDB-initiated updates to previously released 
PDB entries while retaining the same PDB accession code. Updates to 
atomic coordinates, polymer sequence or chemical description in a PDB 
coordinate file will trigger a major version increment. Other changes 
will be classified as minor. All major versions of each PDB structure 
are retained in the new FTP archive.


In the 2018 phase of the project, wwPDB will enable depositor-initiated 
updates of coordinates.


File names in the versioned FTP archive conform to a new naming scheme, 
which allows users to easily see the major and minor version numbers:

__v-..
The familiar 4-character PDB accession code is extended to 8 characters 
prefixed with “pdb”. Thus PDB accession code for entry 1abc becomes 
pdb_1abc. This new format of PDB accession code will be included in 
the model files at a later date. For example, the first initial release 
of PDB entry 1abc would have the following form under the new 
file-naming scheme:

pdb_1abc_xyz_v1-0.cif.gz
where xyz stands for coordinate content; cif indicates the file format; 
and gz indicates a compressed UNIX archive file.
The first minor revision of PDB entry 1abc would then have the following 
name:

pdb_1abc_xyz_v1-1.cif.gz
If PDB entry 1abc then had a major update, it would have the following name:
pdb_1abc_xyz_v2-0.cif.gz (N.B.: The minor update number will be 
reset to zero every time a new major update is made.)
The versioned data files for a particular entry are stored in single 
directory following a 2-character hash from the two penultimate 
characters of the PDB code:

../pdb_versioned/data/entries///
For example, major version 1 with minor version 2 file for entry 1ABC 
would have the following path:

../pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc_xyz_v1-2.cif.gz
Different views of the repository are provided for content type and 
format as a convenience for repository users. The wwPDB provides a link 
to the absolutely latest version files as well as latest version of each 
major version in the entries directories.
For example, users can access the absolute latest version of each 
coordinate mmCIF file (e.g. 1ABC) via below file path.

../pdb_versioned/views/latest/coordinates/mmcif/ab/pdb_1abc/pdb_1abc_xyz.cif.gz
→../pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc_xyz_v2-0.cif.gz
Or users can access all major versions of coordinate mmCIF files for 
entry 1ABC via below file path.

../pdb_versioned/views/all/coordinates/mmcif/ab/pdb_1abc/pdb_1abc_xyz_v1.cif.gz
→../pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc/pdb_1abc_xyz_v1-2.cif.gz
../pdb_versioned/views/all/coordinates/mmcif/ab/pdb_1abc/pdb_1abc/pdb_1abc_xyz_v2.cif.gz
→../pub/pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc_xyz_v2-0.cif.gz
Data files in the current archive location 
ftp://ftp.wwpdb.org/pub/pdb/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
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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] question regarding sequence numbering

[John Berrisford]

h7P_EIdo3UxkBjU=Y-LOBkfQFCKxgiUgTRzNEZXrPFeOzJpt2OOBVMfaQ4Q=>


*Check out my latest paper!!!*

Structural insights into the function of 
<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_WbddCP5AHlUd4=>ZRANB3 
<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_WbddCP5AHlUd4=>in 
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_WbddCP5AHlUd4=>






--
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] Software Engineer / Bioinformatician position at PDBe

[john berrisford]

We are looking for a bioinformatician to integrate value-added 
information on enzymes and catalytic binding sites with the PDB 
structure data and make it available programmatically and via PDBe 
website. The work will involve close collaboration with the Thornton 
research group and with UniProt 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 Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

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

[John Berrisford]

*The model files in the PDB FTP archive have been updated to V5.0 of 
thePDBx/mmCIF dictionary 
<http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/>.Both 
mmCIF <http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/>and 
XML formats have been updated. These files were providedpreviously 
<https://www.wwpdb.org/news/news?year=2017#59089826d3b1d333029d4ea1>for 
the community to review and test. There is no change to PDB format files 
as PDB format is alegacy format 
<https://www.wwpdb.org/documentation/file-formats-and-the-pdb>. These, 
therefore, do not contain all of the remediated information. *


*

The changes to V5.0 include:


 *

   Improvedaudit
   
<http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Groups/audit_group.html>categories
   to capture details of changes to files down to the category level
   for entry revisions.

 *

   Better organized data content
   
<http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Groups/em_group.html>and
   much more extensive metadata in model files for electron microscopy
   derived models.

 *

   Corrected source organism and sequence references for each sequence
   fragment in chimeric proteins.

 *

   Standardized data in several categories, including software name,
   detector name and detector type.

The complete list of changes can be found at thewwPDB website 
<https://www.wwpdb.org/documentation/remediation>.


Questions regarding V5.0 data should 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

[John Berrisford]

ion. Rpim hides this (though tells you more about
the quality of average measurement)

Essentially, for I/sig(I) you can (by and large) adjust your sig(I) values 
however you like if you were so inclined. You can only adjust Rmerge by 
excluding measurements.

I would therefore defend that - amongst the other stats you
enumerate below - it still has a place

Cheers Graeme

On 4 Jul 2017, at 14:10, Keller, Jacob 
<kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>> wrote:

Rmerge does contain information which complements the others.

What information? I was trying to think of a counterargument to what I 
proposed, but could not think of a reason in the world to keep reporting it.

JPK


On 4 Jul 2017, at 12:00, Keller, Jacob 
<kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org><mailto:kell...@janelia.hhmi.org>>
 wrote:

Dear Crystallographers,

Having been repeatedly chagrinned about the continued use and reporting of Rmerge rather 
than Rmeas or similar, I thought of a potential way to promote the change: what if 
merging programs would completely omit Rmerge/cryst/sym? Is there some reason to continue 
to report these stats, or are they just grandfathered into the software? I doubt that any 
journal or crystallographer would insist on reporting Rmerge per se. So, I wonder what 
developers would think about commenting out a few lines of their code, seeing what 
happens? Maybe a comment to the effect of "Rmerge is now deprecated; use Rmeas" 
would be useful as well. Would something catastrophic happen?

All the best,

Jacob Keller

***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email:
kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>
***


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--
John Berrisford
PDBe
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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

[John Berrisford]

Dear CCP4BB

On Tuesday 4th July 2017 at 3.30pm British Summer Time PDBe will be 
presenting a webinar on using our REST API service.


In this webinar we will introduce the PDBe REST API service and show you 
how to access macromolecular structural data programmatically.



This webinar is part 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 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 Software Engineer / Bioinformatician

[John Berrisford]

Dear CCP4BB

PDBe are looking for a software engineer to develop data integration 
pipelines for disparate data sources (all co-located at the EBI) and Web 
components for visualization of this integrated data. In addition, the 
project will involve creation of REST API calls to make this data 
available for the scientific community.


For more details and to apply, please see the listing on the EMBL 
careers site 
(https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj=55746=15470)

<https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj=55746=15470>

The deadline for applications is the 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 webinar - 3D visualisation in your browser

[John Berrisford]

On Wed 22nd February at 1600hrs GMT, the Protein Data Bank in Europe 
(PDBe) is holding a webinar entitled "Visualising protein structures 
online."  Registration is via the following link: 
http://www.ebi.ac.uk/training/events/2017/visualising-protein-structures-online. 



This webinar introduces LiteMol, a new online macromolecular structure 
viewer at PDBe. LiteMol allows you to easily view PDB and EMDB data in 
your web browser. This includes EDS electron density maps from PDBe (1) 
and EM electronic potential maps and even works on mobile devices.


This webinar will also introduce you to how LiteMol shows annotation 
(validation / assemblies / domains) directly on the structure.


For those who cannot watch it live, the webinar will also be available 
shortly after the webinar on the PDBe Youtube channel 
(www.youtube.com/user/ProteinDataBank).


1) 
http://www.ebi.ac.uk/pdbe/about/news/pdbe-brings-electron-density-viewing-masses





--
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PDBe
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European Molecular Biology Laboratory
Wellcome Trust Genome Campus
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Cambridge CB10 1SD UK
Tel: +44 1223 492529

http://www.pdbe.org
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope

[ccp4bb] Powerful new search from pdbe.org

[John Berrisford]

Have you ever searched the PDB and needed to answer questions like these?

 * Which structure is the best for the molecule you are interested in?
 * How many different human proteins have structures solved?
 * Which entries contain your protein bound to DNA?
 * How many different macromolecules have you worked on?
 * Who is using your structure in their work?


The new search system at PDBe.org, using cleaned data and standardised 
vocabularies enables you to answer all these questions easily! Our 
search results show the validation score up front, meaning you can 
assess the quality of a structure at a glance. Four different views of 
the search results enable you to explore the results not only in terms 
of PDB entries and PDB codes, but also by unique macromolecules, 
interacting small molecules and protein sequence families (Pfam).
We also list papers which mention a PDB code, 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
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

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

[John Berrisford]

REMARK 2 is generated from
_refine.ls_d_res_high

http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html

Regards

John

On Wednesday 08 July 2015 15:04:45 Jose Manuel Duarte wrote:
 This looks like the mapping you are after:
 
 http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html
 
 It maps only the structured PDB data items to their equivalent mmCIF
 items. For instance REMARK 2 is not there, but REMARK 200 is. The
 resolution value should then be in REMARK 200 RESOLUTION RANGE HIGH
 (corresponding to mmCIF data item _refine.ls_d_res_high).
 
 Jose
 
 On 07.07.2015 19:05, Phil Jeffrey wrote:
  I'm updating some code to have limited mmCIF/PDB format
  interoperability and have hit a snag.  While I can infer the
  connection between some data items in the PDB header REMARK and the
  items in mmCIF I can't definitively deduce some others.  In particular
  the mapping of
  REMARK  2  RESOLUTION
  seems a little ambiguous and the dictionary documentation doesn't help
  in this regard.
 
  Does anyone know where to find an explicit mapping of one data field
  to another between the two formats ?  (I don't expect there to be a
  data field in the PDB header for everything in mmCIF but I do for the
  reverse case).
 
 
  Thanks
  Phil Jeffrey
  Princeton
 

-- 
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PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
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Tel: +44 1223 492529