[ccp4bb] Software Developer opening position at RCSB PDB (Rutgers)

[Jasmine Young]

RCSB Protein Data Bank is seeking a highly motivated software developer 
with experience in database administration and domain experience in 
computer science or relevant certification. This position will involve 
collaboration with wwPDB scientists and software developers in a 
collaborative team environment. The candidate should be comfortable 
working in a dynamic environment, and able to demonstrate an ability to 
think creatively, generate new ideas, and implement solutions. The 
candidate should be interested in structural biological data and enjoy 
engaging with other programmers and scientists in a collaborative team 
environment.



   Responsibilities:

 * Perform weekly update processes for updating PDB archives
 * Monitor update performance and implement changes for improvements
 * Extend and maintain data exchange with wwPDB partners
 * Improve and maintain weekly update related software/scripts
 * Extend and maintain new content types in the PDB archives
 * Build and support database systems of high availability and quality
 * Design new relational database schema, integrate complex
   bioinformatics data, and improve existing schemas through normalization
 * Improve existing backup processes for both relational and
   non-relational DBMS
 * Provide users with data in appropriate formats and in a timely
   manner for data analysis and statistical reports
 * Indexing and query performance tuning
 * Monitor database performance, implement changes, apply new patches
   and update versions when required
 * Use high-speed transaction recovery techniques for database backups


   Qualifications

 * Bachelor or higher degree in Computer Science or relevant certification
 * DB administration skills in MySQL, MongoDB, and MariaDB
 * Knowledge of data backup, recovery, security, and integrity
 * Experience with software development in Python programming and shell
   scripting
 * Experience with creating and updating DB schemas with complex
   relationships
 * Experience with DB data manipulations (loading, performance
   measurement, backup)


   Additional Skills are a Plus

 * Experience working with large and complex scientific datasets and
   data models
 * Experience working with a DBMS in both on-cloud and on-premise
   environments
 * Experience in C++ programming
 * Problem solving skills and ability to think algorithmically
 * Excellent interpersonal, verbal, and written communication skills


   Outstanding Benefits Package

RCSB PDB is a friendly and collaborative working environment with 
excellent professional development opportunities. At Rutgers, this 
academic position offers New Jersey state benefits and a faculty-level 
salary. There are personal rewards including comprehensive health and 
retirement plan options.


For more details about state and university benefits, see our employee 
benefits page 
<https://uhr.rutgers.edu/benefits/alternate-benefit-program-abp>.



   About RCSB PDB:

RCSB PDB impacts millions rcsb.org users around the world working in 
fundamental biology, biomedicine, bioengineering, and energy sciences. 
Our work involves data analysis, integration, transformation, and 
presentation/visualization of data using complex interactive graphical 
user interfaces. An important aspect is to provide users with the 
ability to search and explore the PDB data archive. Solutions are 
implemented using a wide range of components developed and maintained 
in-house, in addition to third-party tools, libraries, frameworks and 
technologies.


See *Why Join Us* <https://www.rcsb.org/pages/jobs#whyJoinUs>.

Apply at Rutgers: https://jobs.rutgers.edu/postings/208687


--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Postdoctoral Associate position available at RCSB PDB (Rutgers)

[Jasmine Young]

   Summary

RCSB Protein Data Bank is seeking a highly motivated postdoctoral 
researcher with domain expertise in organometallic complexes. The 
successful candidate will work on the metalloprotein remediation project 
that leads to modernized and uniform data representation of PDB entries 
containing metalloproteins to make these data Findable, Accessible, 
Interoperable and Reusable (FAIR). This position will involve 
collaboration with wwPDB scientists and software developers in a 
collaborative team environment. Training will be provided in the design 
of PDB data model, PDB small molecule reference dictionaries, PDB 
chemical tools, and other related scientific software tools used in 
structural biology. The candidate should show an eagerness to learn new 
skills and technologies.


She/he will be expected to contribute to this project by

 * defining the scope of this project through identification of
   existing PDB entries that contain metalloproteins
 * conducting scientific review on organometallic complexes in the PDB
   entries and identifying issues in the current data representation
   and chemical definitions
 * creating solutions to overcome current challenges including
   establishing new data representation and improving chemical
   definitions in the PDB small molecule references
 * collaborating with software developers and biocurators on validating
   solutions and software testing


   Minimal Education and Experience

 * PhD in Chemistry, Cheminformatics, or chemistry related disciplines
 * Has domain expertise in organometallic complexes
 * Excellent interpersonal, verbal, and written communication skills
 * Good documentation habits


   Additional Skills are a Plus

 * Experience in small molecule crystallography
 * Experience in macromolecular structures
 * Experience working with large and complex scientific datasets
 * Self-motivation and independence
 * A track record of productive research results


   Outstanding Benefits Package

RCSB PDB is located at Rutgers, State University of New Jersey and 
provides a friendly and collaborative working environment with excellent 
professional development opportunities. At Rutgers, this academic 
position offers New Jersey state benefits. There are personal rewards 
including comprehensive health and retirement plan options. See *Why 
Join Us* <https://www.rcsb.org/pages/jobs#whyJoinUs>.


For more details about state and university benefits, see our employee 
benefits page 
<https://uhr.rutgers.edu/benefits/alternate-benefit-program-abp>.


Apply
https://jobs.rutgers.edu/postings/189038


--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Ligand Expo: Scheduled downtime and request for feedback

[Jasmine Young]

Dear CCP4 users,

Ligand Expo (http://ligand-expo.rcsb.org) will be down during the month 
of January 2023. Requests to this service will return a 410 http error 
code (“Gone”) and a message to contact RCSB PDB with any questions.


Users can access CCD data in mmCIF format at 
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/ hashed with the last 
character position, e.g.,


https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/TRP/ 
<https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/TRP/>



--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Ligand Expo: Scheduled downtime and request for feedback

[Jasmine Young]

Ligand Expo (http://ligand-expo.rcsb.org) will be down during the month 
of January 2023. Requests to this service will return a 410 http error 
code (“Gone”) and a message to contact RCSB PDB with any questions.


Please help us better understand which Ligand Expo features are utilized 
and should be integrated with RCSB.org by taking this survey 
<https://www.surveymonkey.com/r/FHSPWWZ>.


--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] DNS name changes for PDB archive downloads from wwPDB

[Jasmine Young]

wwPDB has introduced DNS names for programmatic access to PDB archive 
downloads:


 * FTP: ftp://ftp.wwpdb.org
 * HTTPS: https://files.wwpdb.org (replaces https://ftp.wwpdb.org)
 * RSYNC: rsync://rsync.wwpdb.org (replaces rsync://wwpdb.org)

The PDB Archive Downloads <http://www.wwpdb.org/ftp/pdb-ftp-sites> 
documentation has detailed information.


Starting September 2023, wwPDB will start enforcing use of these updated 
DNS names. URLs in which the DNS name doesn’t match the protocol (e.g., 
https://ftp.wwpdb.org, ftp://files.wwpdb.org) will no longer work at 
that time.


Users who download PDB archive data programmatically are encouraged to 
switch to the new DNS names as soon as possible. HTTPS protocol is 
preferred (over FTP) for individual file downloads.


Please contact i...@wwpdb.org with any questions.


--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Developers & PostDocs: Join RCSB PDB to participate in exciting projects with significant impact on the scientific community

[Jasmine Young]

*Now the URL link is provided.*

RCSB Protein Data Bank (RCSB.ORG) is seeking highly motivated scientific 
software developers and postdoctoral researchers with domain experience 
in structural biology, bioinformatics or related fields. Candidates 
should be interested in structural biological data and enjoy engaging 
with other programmers and scientists in a collaborative team environment.


Several positions for scientific software developers, postdoctoral 
researchers, and web application developers are available at RCSB PDB 
Rutgers, SDSC/UCSD, and UCSF.


Develop innovative analysis, integration, query, and visualization tools 
for 3D biomolecular structures at RCSB.org to help accelerate research 
and training in biology, medicine, and related disciplines.


Design, develop, & deploy modern web and data applications & complex 
user interfaces. Help accelerate research and training in biology, 
medicine, & related disciplines.


Find out more and apply for any of these positions at 
https://www.rcsb.org/pages/jobs <https://www.rcsb.org/pages/jobs>.


 * Scientific/Bioinformatics Software Developer at RCSB PDB (Rutgers)
 * Scientific Web Application Developer (Rutgers)
 * Scientific Software Developer (UCSD)
 * Postdoctoral Researcher (UCSD)
 * Postdoctoral Researcher (UCSF)


Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 2/17/22 9:45 AM, Jasmine Young wrote:


RCSB Protein Data Bank (RCSB.ORG) is seeking highly motivated 
scientific software developers and postdoctoral researchers with 
domain experience in structural biology, bioinformatics or related 
fields. Candidates should be interested in structural biological data 
and enjoy engaging with other programmers and scientists in a 
collaborative team environment.


Several positions for scientific software developers, postdoctoral 
researchers, and web application developers are available at RCSB PDB 
Rutgers, SDSC/UCSD, and UCSF.


Develop innovative analysis, integration, query, and visualization 
tools for 3D biomolecular structures at RCSB.org to help accelerate 
research and training in biology, medicine, and related disciplines.


Design, develop, & deploy modern web and data applications & complex 
user interfaces. Help accelerate research and training in biology, 
medicine, & related disciplines.


  * Scientific/Bioinformatics Software Developer at RCSB PDB (Rutgers)
  * Scientific Web Application Developer (Rutgers)
  * Scientific Software Developer (UCSD)
  * Postdoctoral Researcher (UCSD)
  * Postdoctoral Researcher (UCSF)


--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Developers & PostDocs: Join RCSB PDB to participate in exciting projects with significant impact on the scientific community

[Jasmine Young]

RCSB Protein Data Bank (RCSB.ORG) is seeking highly motivated scientific 
software developers and postdoctoral researchers with domain experience 
in structural biology, bioinformatics or related fields. Candidates 
should be interested in structural biological data and enjoy engaging 
with other programmers and scientists in a collaborative team environment.


Several positions for scientific software developers, postdoctoral 
researchers, and web application developers are available at RCSB PDB 
Rutgers, SDSC/UCSD, and UCSF.


Develop innovative analysis, integration, query, and visualization tools 
for 3D biomolecular structures at RCSB.org to help accelerate research 
and training in biology, medicine, and related disciplines.


Design, develop, & deploy modern web and data applications & complex 
user interfaces. Help accelerate research and training in biology, 
medicine, & related disciplines.


 * Scientific/Bioinformatics Software Developer at RCSB PDB (Rutgers)
 * Scientific Web Application Developer (Rutgers)
 * Scientific Software Developer (UCSD)
 * Postdoctoral Researcher (UCSD)
 * Postdoctoral Researcher (UCSF)


--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Scientific/Bioinformatics Software Developer position at RCSB PDB (Rutgers)

[Jasmine Young]

Dear CCP4bb,

RCSB Protein Data Bank is seeking highly motivated, scientific software 
developers with domain experience in structural biology, bioinformatics 
or related fields. The candidate should be interested in structural 
biological data and enjoy engaging with other programmers and scientists 
in a collaborative team environment.



   Responsibilities:

 * Design, development, and deployment of modern data-intensive
   scientific applications, within a microservice architecture
 * Integration of complex bioinformatics data, implementation of
   specialised algorithms for search/data analysis and use of AI tools
 * Design and implementation of cloud-ready deployments using
   containerization and modern cloud technologies
 * Analysis, refactoring and adaptation of legacy code to conform to
   new architecture designs
 * Debugging, testing, troubleshooting


   Qualifications:

 * PhD or Master’s degree in Computer Science, Biochemistry,
   Bioinformatics, or a related discipline, or a comparable combination
   of education and experience developing modern scientific data
   applications
 * Excellent interpersonal, verbal, and written communication skills
 * Experience with Python, document databases (e.g., MongoDB), search
   and data access tools (e.g., ElasticSearch and GraphQL)

Scientific background in any of the following areas would be considered 
a major plus: Molecular Biology, Bioinformatics, Cheminformatics, 
Biochemistry, Chemistry, Genomics.


Experience working with large and complex scientific datasets would also 
be considered a plus.



   Outstanding Benefits Package

RCSB PDB is a friendly and collaborative working environment with 
excellent professional development opportunities. At Rutgers, this 
academic position offers New Jersey state benefits and a faculty-level 
salary. There are personal rewards including comprehensive health and 
retirement plan options.



   About RCSB PDB:

The work at RCSB PDB (rcsb.org) focuses on data analysis, integration, 
and transformation, and the presentation and visualization of data using 
complex interactive graphical user interfaces. An important aspect is to 
provide users with the ability to search and explore the PDB data 
archive. Solutions are implemented using a wide range of components 
developed and maintained in-house, in addition to third-party tools, 
libraries, frameworks and technologies. The candidate should be 
comfortable working in a dynamic environment, and able to demonstrate an 
ability to think creatively, generate new ideas, and implement 
solutions. The candidate should also show an eagerness to learn new 
skills and technologies.



   Apply at Rutgers:

https://jobs.rutgers.edu/postings/142529


--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Jasmine Young]

Dear all,

Extensions to the PDBx/mmCIF dictionary for reflection data with 
anisotropic diffraction limits, for unmerged reflection data, and for 
quality metrics of anomalous diffraction data are now supported in OneDep.


In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group 
<https://www.wwpdb.org/task/mmcif> was convened to develop a richer 
description of experimental data and associated data quality metrics. 
Members of this Data Collection and Processing Subgroup are all actively 
engaged in development and support of diffraction data processing 
software. The Subgroup met virtually for several months discussing, 
reviewing, and finalizing a new set dictionary content extension that 
were incorporated into the PDBx/mmCIF dictionary 
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/> on 
February 16, 2021. A reference implementation of the new content 
extensions has been developed by Global Phasing Ltd. 
<https://www.globalphasing.com/>


These extensions facilitate the deposition and archiving of a broader 
range of diffraction data, as well as new quality metrics pertaining to 
these data. These extensions cover three main areas:


1. scaled and merged reflection data that have been processed to take
   account of diffraction anisotropy, by providing descriptors for that
   anisotropy, in terms of (1) a parameter-free definition of a cut-off
   surface by means of a per-reflection “signal” and a threshold value
   for that signal, and (2) the ellipsoid providing the best fit to the
   resulting cut-off surface;
2. scaled and unmerged reflection data, by providing extra item
   definitions aimed at ensuring that such data can be meaningfully
   re-analysed, and their quality assessed independently from the
   associated model, after retrieval from the archive;
3. anomalous diffraction data, by adding descriptors for numerous
   relevant, but previously missing, statistics.

The new mmCIF data extensions describing anisotropic diffraction now 
enable archiving of the results of Global Phasing’s STARANISO program. 
Developers of other software can make use of them or extend the present 
definitions to suit their applications. Example files created by 
autoPROC, BUSTER (version 20210224 
<https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif>) 
and Gemmi that are compliant with the new dictionary extensions are 
provided in a GitHub repository 
<https://github.com/pdbxmmcifwg/onedep-extended-sf-support-examples.git>.


These example files, and similarly compliant files produced by other 
data processing and/or refinement programs, are suitable for direct 
uploading to the wwPDB OneDep system. Automatic recognition of that 
compliance, implemented by means of explicit dictionary versioning using 
the new pdbx_audit_conform record, will avoid unnecessary pre-processing 
at the time of deposition. This improved OneDep support will ensure a 
lossless round trip between data processing/refinement in the lab and 
deposition at the PDB.


wwPDB strongly encourages structural biologists to always use the latest 
versions of structure determination software packages to produce data 
files for PDB deposition. wwPDB also encourages crystallographers 
wishing to deposit new structures together with their associated 
diffraction data to use the software which guarantees consistency 
between data and final model. This consistency is difficult to achieve 
when separate diffraction data files and model coordinate files are 
pieced together /a posterior/i by /ad hoc/ means.


wwPDB also encourages depositors to make their raw diffraction images 
available from one of the public repositories 
<https://www.wwpdb.org/deposition/faq#start> to allow direct access to 
the original diffraction image data.



--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Carbohydrate Remediation Paper Published in Glycobiology

[Jasmine Young]

Dear all,

Carbohydrate molecules present in more than 14,000 PDB structures were 
reviewed and remediated to conform to a new standardized format to 
facilitate broader usage of the resource by the glycoscience community 
and researchers studying glycoproteins.


   Modernized uniform representation of carbohydrate molecules in the 
Protein Data Bank

   Chenghua Shao, Zukang Feng, John D Westbrook, Ezra Peisach, John
   Berrisford, Yasuyo Ikegawa, Genji Kurisu, Sameer Velankar, Stephen K
   Burley, Jasmine Y Young
   (2021) /Glycobiology/ 31: 1204–1218,
https://doi.org/10.1093/glycob/cwab039

Additional documentation about the carbohydrate remediation project is 
also available, 
http://www.wwpdb.org/documentation/carbohydrate-remediation.



--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Biocurator Milestone: >10,000 Depositions Processed

[Jasmine Young]

Congratulations to the wwPDB biocurator Dr. Brian Hudson on processing 
over 10,000 PDB depositions!


Dr. Hudson received his PhD in Chemistry from the California Institute 
of Technology and has an expertise in X-ray crystallography and 
cryo-electron microscopy. He has joined PDB in 2010 and has established 
himself as a highly qualified professional with deep understanding of 
scientific data and various experimental techniques and dedication to 
exceptional quality data curation. He was one of the EM data curation 
pioneers who curated over 1000 of EM map entries before the OneDep 
system was established.


We congratulate Dr. Hudson with this exciting accomplishment and look 
forward to his further career success!


RCSB PDB Biocurator Dr. Brian P. Hudson talking about the SARS-CoV-2 
main protease in February 2020:


https://www.rutgers.edu/news/how-rutgers-team-working-crack-coronavirus-code


--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Scientific/Bioinformatics Software Developer at RCSB PDB (Rutgers)

[Jasmine Young]

   Dear all,

RCSB Protein Data Bank is seeking highly motivated, scientific software 
developers with domain experience in structural biology, bioinformatics 
or related fields. The candidate should be interested in structural 
biological data and enjoy engaging with other programmers and scientists 
in a collaborative team environment.



   Responsibilities:

 * Design, development, and deployment of modern data-intensive
   scientific applications, within a microservice architecture
 * Integration of complex bioinformatics data, implementation of
   specialised algorithms for search/data analysis and use of AI tools
 * Design and implementation of cloud-ready deployments using
   containerization and modern cloud technologies
 * Analysis, refactoring and adaptation of legacy code to conform to
   new architecture designs
 * Debugging, testing, troubleshooting


   Qualifications:

 * PhD or Master’s degree in Computer Science, Biochemistry,
   Bioinformatics, or a related discipline, or a comparable combination
   of education and experience developing modern scientific data
   applications
 * Excellent interpersonal, verbal, and written communication skills
 * Experience with Python, document databases (e.g., MongoDB), search
   and data access tools (e.g., ElasticSearch and GraphQL)

Scientific background in any of the following areas would be considered 
a major plus: Molecular Biology, Bioinformatics, Cheminformatics, 
Biochemistry, Chemistry, Genomics.


Experience working with large and complex scientific datasets would also 
be considered a plus.



   Outstanding Benefits Package

RCSB PDB is a friendly and collaborative working environment with 
excellent professional development opportunities. At Rutgers, this 
academic position offers New Jersey state benefits and a faculty-level 
salary. There are personal rewards including comprehensive health and 
retirement plan options.



   About RCSB PDB:

The work at RCSB PDB (rcsb.org) focuses on data analysis, integration, 
and transformation, and the presentation and visualization of data using 
complex interactive graphical user interfaces. An important aspect is to 
provide users with the ability to search and explore the PDB data 
archive. Solutions are implemented using a wide range of components 
developed and maintained in-house, in addition to third-party tools, 
libraries, frameworks and technologies. The candidate should be 
comfortable working in a dynamic environment, and able to demonstrate an 
ability to think creatively, generate new ideas, and implement 
solutions. The candidate should also show an eagerness to learn new 
skills and technologies.



   Apply at Rutgers:

https://jobs.rutgers.edu/postings/142529


--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Scientific Data Application Developer at RCSB PDB (Rutgers)

[Jasmine Young]

RCSB PDB is looking for a highly motivated, scientific developer with 
domain experience in structural biology or bioinformatics or related 
fields. The candidate should be interested in structural biological data 
and enjoy engaging with other developers and scientists in a 
collaborative team environment.


The work at RCSB PDB focuses on data analysis, integration, and 
transformation, and the presentation and visualization of data using 
complex interactive graphical user interfaces. An important aspect is to 
provide users with the ability to search and explore the PDB data 
archive. Solutions are implemented using a wide range of components 
developed and maintained in-house, in addition to third-party tools, 
libraries, frameworks and technologies. The candidate should be 
comfortable working in a fast-changing environment, and able to 
demonstrate an ability to think creatively, generate new ideas, and 
implement solutions. The candidate should also show an eagerness and 
willingness to learn new skills and technologies.



   Requirements

The candidate should have experience working with Python, document 
databases (e.g. MongoDB), search and data access tools (e.g., 
ElasticSearch and GraphQL).


Scientific background in any of the following areas would be considered 
a major plus: Molecular Biology, Bioinformatics, Biochemistry, 
Chemistry, Genomics.


Experience working with large and complex scientific datasets would also 
be considered a plus.


While a scientific background is not an absolute requirement for the 
position, the candidate should indicate an interest in engaging with 
scientists and scientific content, and in working in an 
academic/research environment.



   Job Description

Responsibilities for this position will include:

 * Design, development, and deployment of modern data applications.
 * Analysis, refactoring and adaptation of legacy code to conform to
   new architecture designs.
 * Debugging, testing, troubleshooting.

Qualifications:

 * PhD or Masters degree in Computer Science, Biochemistry,
   Bioinformatics, or a related discipline, or a comparable combination
   of education and experience developing modern scientific data
   applications.
 * Excellent interpersonal, verbal, and written communication skills.


   Apply at RCSB PDB:

RCSB PDB is a friendly and collaborative working environment with 
excellent professional development opportunities. At Rutgers, this 
academic position offers New Jersey state benefits and a faculty-level 
salary.


Apply at https://jobs.rutgers.edu/postings/142529



--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Consistent Format for Validation and Coordinate Data in the PDB archive

[Jasmine Young]

wwPDB validation reports are now provided in PDBx/mmCIF format for all 
new depositions in OneDep. This change makes validation data more 
interoperable with the PDB archival format. Data are more logically and 
better organized in the PDBx/mmCIF reports, and therefore more 
“database-friendly” than the report in XML format. PDBx/mmCIF-format 
validation reports for newly released and modified entries will be 
distributed through the PDB 
<https://ftp.wwpdb.org/pub/pdb/validation_reports/> and EMDB 
<https://ftp.wwpdb.org/pub/emdb/validation_reports/> Core Archives.


The new PDBx/mmCIF reports are easier to interpret. They contain a 
high-level summary and offer easier access to residue-level information. 
Data are provided at multiple levels: entity, chain-specific, and even 
at the individual residues. For example, it is more straightforward to 
obtain the total number of clashes. The corresponding validation 
dictionary is available at 
mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Index 
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Index/>. 
Examples of PDBx/mmCIF validation reports for X-ray, 3DEM, and NMR are 
publicly available at GitHub 
<https://github.com/wwPDB/validation-mmcif-examples>.


PDBx/mmCIF validation reports will be provided for the full PDB and EMDB 
archives once archival validation recalculation is performed.


wwPDB strongly recommends all PDB users and software developers adopt 
this format for future applications.



--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Future Planning: Entries with extended PDB and CCD ID codes will be distributed in PDBx/mmCIF format only

[Jasmine Young]

http://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d

wwPDB, in collaboration with the PDBx/mmCIF Working Group 
<http://www.wwpdb.org/task/mmcif>, has set plans to extend the length of 
ID codes for PDB and Chemical Component Dictionary (CCD) ID entries in 
the future. Entries issued with these extended IDs will not be supported 
by the legacy PDB file format.


CCD entries are currently identified by unique three-character 
alphanumeric codes. At current growth rates, we anticipate running out 
of available new codes in the next three to four years. At this point, 
the wwPDB will issue four-character alphanumeric codes for CCD IDs in 
the OneDep system. Due to constraints of the legacy PDB file format, 
entries containing these new, four character ID codes will only be 
distributed in PDBx/mmCIF format. The wwPDB will begin implementation of 
extended CCD ID codes in 2022.


In addition, wwPDB also plans extended PDB ID length to eight characters 
prefixed by ‘PDB’, e.g., pdb_1abc. Each PDB ID has a corresponding 
Digital Object Identifier (DOI), often required for manuscript 
submission to journals and described in publications by the structure 
authors. Both extended PDB IDs and corresponding PDB DOIs, along with 
existing four character PDB IDs, will be included in the PDBx/mmCIF 
formatted files for all new entries by Fall 2021.


For example, PDB entry 1ABC will also have the extended PDB ID 
(pdb_1abc) and the corresponding PDB DOI (10.2210/pdb1abc/pdb) 
listed in the _database_2 PDBx/mmCIF category.


loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB   1abc pdb_1abc 10.2210/pdb1abc/pdb
WWPDB   D_1x     ?       ?

Once four-character PDB IDs are all consumed, newly-deposited PDB 
entries will only be issued extended PDB ID codes, and entries will only 
be distributed in PDBx/mmCIF format.


wwPDB is asking PDB users and related software developers to review code 
and begin to remove such limitations for the future.


--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] OneDep highlights curated assemblies for review in Mol*

[Jasmine Young]

To improve the clarity of assembly definitions in curation, wwPDB now 
makes curated PDB assemblies available for depositors to view in OneDep 
using the Mol* viewer.


One of the important processes in curation of PDB entries is the 
definition of assemblies for each structure. This helps users of PDB 
data to understand the structure in the context of its complex formation 
in the specific experimental conditions.


To ensure that assemblies are curated correctly, they are reviewed by 
annotators at the time of curation before being reported back to the 
depositors after the curation process.


The deposition system in OneDep has now been enhanced so that after 
curation, the annotated assembly is displayed in the Mol* 3D viewer 
<https://molstar.org/> for depositors to review. This viewer is 
available in a new Review section in the deposition interface, which is 
present after curation of the entry. The Mol* viewer can display PDB 
structure data within the browser with minimal memory requirements, 
therefore making it quick and easy to visually display assembly information.


These changes will help improve the validation and reporting of curated 
assemblies during the deposition process.



The assembly review page, as displayed for depositors after curation of 
the entry. The curated assembly is displayed in the Mol* 3D viewer, 
within the browser.
The assembly review page, as displayed for depositors after curation of 
the entry. The curated assembly is displayed in the Mol* 3D viewer, 
within the browser.



http://www.wwpdb.org/news/news?year=2021#604a58800769342b1f3d04b1
<http://www.wwpdb.org/news/news?year=2021#top>

--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Improved support for extended PDBx/mmCIF structure factor files in OneDep

[Jasmine Young]

Extensions to the PDBx/mmCIF dictionary for reflection data with 
anisotropic diffraction limits, for unmerged reflection data, and for 
quality metrics of anomalous diffraction data are now supported in OneDep.


In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group 
<https://www.wwpdb.org/task/mmcif> was convened to develop a richer 
description of experimental data and associated data quality metrics. 
Members of this Data Collection and Processing Subgroup are all actively 
engaged in development and support of diffraction data processing 
software. The Subgroup met virtually for several months discussing, 
reviewing, and finalizing a new set dictionary content extension that 
were incorporated into the PDBx/mmCIF dictionary 
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/> on 
February 16, 2021. A reference implementation of the new content 
extensions has been developed by Global Phasing Ltd. 
<https://www.globalphasing.com/>


These extensions facilitate the deposition and archiving of a broader 
range of diffraction data, as well as new quality metrics pertaining to 
these data. These extensions cover three main areas:


1. scaled and merged reflection data that have been processed to take
   account of diffraction anisotropy, by providing descriptors for that
   anisotropy, in terms of (1) a parameter-free definition of a cut-off
   surface by means of a per-reflection “signal” and a threshold value
   for that signal, and (2) the ellipsoid providing the best fit to the
   resulting cut-off surface;
2. scaled and unmerged reflection data, by providing extra item
   definitions aimed at ensuring that such data can be meaningfully
   re-analysed, and their quality assessed independently from the
   associated model, after retrieval from the archive;
3. anomalous diffraction data, by adding descriptors for numerous
   relevant, but previously missing, statistics.

The new mmCIF data extensions describing anisotropic diffraction now 
enable archiving of the results of Global Phasing’s STARANISO program. 
Developers of other software can make use of them or extend the present 
definitions to suit their applications. Example files created by 
autoPROC, BUSTER (version 20210224 
<https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif>) 
and Gemmi that are compliant with the new dictionary extensions are 
provided in a GitHub repository 
<https://github.com/pdbxmmcifwg/onedep-extended-sf-support-examples.git>.


These example files, and similarly compliant files produced by other 
data processing and/or refinement programs, are suitable for direct 
uploading to the wwPDB OneDep system. Automatic recognition of that 
compliance, implemented by means of explicit dictionary versioning using 
the new pdbx_audit_conform record, will avoid unnecessary pre-processing 
at the time of deposition. This improved OneDep support will ensure a 
lossless round trip between data processing/refinement in the lab and 
deposition at the PDB.


wwPDB strongly encourages structural biologists to always use the latest 
versions of structure determination software packages to produce data 
files for PDB deposition. wwPDB also encourages crystallographers 
wishing to deposit new structures together with their associated 
diffraction data to use the software which guarantees consistency 
between data and final model. This consistency is difficult to achieve 
when separate diffraction data files and model coordinate files are 
pieced together /a posterior/i by /ad hoc/ means.


wwPDB also encourages depositors to make their raw diffraction images 
available from one of the public repositories 
<https://www.wwpdb.org/deposition/faq#start> to allow direct access to 
the original diffraction image data.



<http://www.wwpdb.org/news/news?year=2021#top>

--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

[Jasmine Young]

A new article in /Structure/ <https://doi.org/10.1016/j.str.2021.02.004> 
describes new features, including branched representations and 2D SNFG 
images for carbohydrates, identification of ligands of interest, 3D 
views of electron density fit, and 2D images of small molecule geometry.


These enhancements and processes for validation of 3D small-molecular 
structures reflect recommendations from the wwPDB/CCDC/D3R Ligand 
Validation Workshop and the adoption of software through community 
collaborations.


This manuscript also highlights enhancements made since the initial 
implementation of Validation Reports as described in Validation of the 
Structures in the Protein Data Bank (2017) Structure 25: 1916-1927 doi: 
10.1016/j.str.2017.10.009 <https://doi.org/10.1016/j.str.2017.10.009>.


*Enhanced Validation of Small-Molecule Ligands and Carbohydrates in the 
Protein Data Bank *
Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, Gérard 
Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko 
F. Aoki-Kinoshita, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, 
Stephen K. Burley, and Jasmine Y. Young
(2021) Structure doi: 10.1016/j.str.2021.02.004 
<https://doi.org/10.1016/j.str.2021.02.004>


undefined <https://doi.org/10.1016/j.str.2021.02.004>

<http://www.wwpdb.org/news/news?year=2021#top>

--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Jasmine Young]

Dear Marcin,

Thank you for your feedback. We will improve mmCIF documentation for 
this recommendation.


Most of the wwPDB remediation do not require change of chain id or 
residue numbering. For new data representation such as carbohydrates and 
previous remediation of peptide-like inhibitors, it is unpreventable to 
change original chain id and/or numbering. In this case, wwPDB provides 
a mapping category to retain original chain id or residue numbering.



Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 12/11/20 8:11 AM, Marcin Wojdyr wrote:

Dear Jasmine,

I fully agree with this recommendation:


To use the wwPDB-assigned chain ID in publications,
_atom_site.auth_seq_id _atom_site.auth_comp_id, and
_atom_site.auth_asym_id can be used for the residue number, residue ID,
and chain ID, respectively.

It would help a lot if the same was recommended in the mmCIF documentation.
Currently, these IDs are described as non-mandatory, alternative IDs,
which suggests (to those few software developers that read the
documentation) that they shouldn't be relied upon.

It'd also be good if the IDs that are recommended for use in
publications weren't changed afterwards as it happened in this
remediation.
Carbohydrate remediation was indeed consulted with the community over
a long time, but perhaps this particular change wasn't made clear. I
always assumed that only the primary (wwPDB internal) IDs are to be
changed, not the ones that were used in publications.

Best regards,
Marcin




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Jasmine Young]

Dear Marcin,

The cif item, _pdbx_branch_scheme.pdb_asym_id, in the pdbx_branch_scheme 
category is a pointer to _atom_site.auth_asym_id in the atom_site 
category (I know this is confusing). The labels are consistently defined 
as the ones in _pdbx_poly_seq_scheme and _pdbx_nonpoly_scheme.


To use the wwPDB-assigned chain ID in publications, 
_atom_site.auth_seq_id _atom_site.auth_comp_id, and 
_atom_site.auth_asym_id can be used for the residue number, residue ID, 
and chain ID, respectively.



Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 12/9/20 4:31 PM, Marcin Wojdyr wrote:

Dear Jasmine,

thank you for this explanation. It's the best explanation of this
remediation I've read.

The use of IDs may confuse people, so I'd like to reiterate it and ask
for clarification.
Every residue in the mmCIF format has three (3) independent chain IDs
assigned to it (and three sequence numbers, and three residue names).

In your example:
J 4 NAG 1 I NAG 1 A NAG 1310 n

J - asym_id = _atom_site.label_asym_id
I - pdb_asym_id = _atom_site.auth_asym_id (?!)
A - auth_asym_id = n/a

(correct me if I got it wrong, but I see that _atom_site.auth_asym_id
corresponds to _pdbx_branch_scheme.pdb_asym_id and not to auth_asym_id
as one could expect).

How to call these chain IDs? When I write software documentation, I
need to refer to chain IDs (and sequence numbers), but I can't find
proper words to clearly tell which ID I'm referring to. I was using
hard to read names such as auth_asym_id, but now I see that even this
is ambiguous.

BTW, when you write that wwPDB encourages depositors to use the
wwPDB-assigned chain ID in publications, which of the two
wwPDB-assigned chain IDs do you mean?

Thank you,
Marcin




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Jasmine Young]

Dear Robbie,

In the case that only single monosaccharide was modelled at 
glycosylation site with a known oligosaccharide sequence, technically 
the software cannot generate glycosidic linkages, linear descriptors for 
sequences, 2D SNFG images, etc. Therefore, this single monosaccharide 
cannot be represented as a branched entity. However, if an author 
provides PDB an updated coordinates with additional monosaccharides 
modeled that bounds to the original monosaccharide, the software will 
automatically detect this linkage and convert non-polymer entity of the 
original monosaccharide into a branched entity (vice versa).



Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 12/9/20 4:35 AM, Robbie Joosten wrote:


Dear Jasmine,

I have a few questions about this bit:

//

As some users pointed out, single NAG could be just a part of the 
glycan that the author chose to build, as most natural N-glycans must 
have stem of a common core of 5 monosaccharides or its fucosylated 
version, such as those modeled in the PDB ID 6WPS. However, the PDB is 
a 3D-atomic coordinate archive in which the model coordinates are 
built based on supporting experimental data. Therefore, carbohydrates 
are described as-is in the modeled structures without reference to 
missing components of the presumed oligosaccharide sequence. If the 
author only builds a monosaccharide, then this monosaccharide is 
described as a non-polymer ligand.


//

Is it technically allowed to have a single, covalently bound 
carbohydrate described as a branched entity of length 1?


If so, if an author does specify such a single modeled residue as 
branched entity, for instance because (s)he has a good reason to 
suspect that a second residue was there, but isn’t comfortable with 
building it, then is this specification kept in annotation?


If not, do you expect model building programs to switch from branched 
to non-poly entities when a second residue is removed when a model is 
written out? And back again when a residue is added? I find this 
rather unpractical from an implementation point of view. We change 
carbohydrate trees quite regularly.


Cheers,

Robbie

*From:*CCP4 bulletin board  *On Behalf Of 
*Jasmine Young

*Sent:* Tuesday, December 8, 2020 21:01
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at 
the PDB -- N-glycans are now separate chains if more than one residue


Dear PDB Data Users:

Thank you for providing feedback on the results of an archival-level 
carbohydrate remediation project that led to the re-release of over 
14,000 PDB structures in July 2020. This update includes diverse 
oligosaccharides: glycosylation; metabolites such as maltose, sucrose, 
cellulose fragments; glycosaminoglycans, such as fragments of heparin 
and heparan sulfate; epitope patterns such as A/B blood group antigens 
and the H-type or Lewis-type stems; and many artificial carbohydrates 
mimicking or counting natural products 
(https://www.wwpdb.org/documentation/carbohydrate-remediation 
<https://www.wwpdb.org/documentation/carbohydrate-remediation>).


Starting in 2017, this PDB remediation aimed to standardize the 
biochemical nomenclature of the carbohydrate components following the 
IUPAC-IUBMB recommendations established by the carbohydrate community 
(https://media.iupac.org/publications/pac/1996/pdf/6810x1919.pdf 
<https://media.iupac.org/publications/pac/1996/pdf/6810x1919.pdf>), 
and to provide uniform representation of oligosaccharides to improve 
the identification and searchability of oligosaccharides modeled in 
the PDB structures.  During the remediation planning, wwPDB consulted 
community users and the PDBx/mmCIF Working Group and made data files 
available on GitHub in early 2020 for community feedback. wwPDB has 
collaborated with Robert Woods at University of Georgia in US, 
researchers at The Noguchi Institute and Soka University in Japan, and 
Thomas Lutteke in Germany to generate uniform linear descriptors for 
the oligosaccharide sequences.


To achieve these community goals, each oligosaccharide is represented 
as a branched entity with complete biochemical description and each 
glycosidic linkage specified. The full representation of carbohydrates 
is provided in the mmCIF format file, but this is not possible in 
legacy PDB format files (as the format has been frozen since 2012 
(https://www.wwpdb.org/documentation/file-formats-and-the-pdb 
<https://www.wwpdb.org/documentation/file-formats-and-the-pdb>).


Proper indexing is necessary for branched entity representation a

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Jasmine Young]

O O3 . NAG Y  6 .    ? 190.069 159.774 209.231 1.00 47.22  
? 1301 NAG A O3  1


HETATM 27665 O O4 . NAG Y  6 .    ? 187.867 159.778 207.435 1.00 48.89  
? 1301 NAG A O4  1


HETATM 27666 O O5 . NAG Y  6 .    ? 189.760 162.757 206.285 1.00 47.83  
? 1301 NAG A O5  1


HETATM 27667 O O6 . NAG Y  6 .    ? 186.953 163.102 206.622 1.00 49.06  
? 1301 NAG A O6  1


HETATM 27668 O O7 . NAG Y  6 .    ? 192.879 162.950 209.739 1.00 47.58  
? 1301 NAG A O7  1


...

#


Author-provided chain ID and residue numbering for oligosaccharides are 
retained in the PDBx/mmCIF file (_pdbx_branch_scheme.auth_mon_id and 
_pdbx_branch_scheme.auth_seq_num, respectively). Users can map how 
carbohydrates are described in the corresponding primary citation to the 
PDBx/mmCIF files using _pdbx_branch_scheme mapping category. wwPDB 
strongly encourages depositors to use the wwPDB-assigned chain ID and 
residue numbers in any publication material.


For example, PDB entry 6WPS

#

loop_

*_pdbx_branch_scheme.asym_id *

_pdbx_branch_scheme.entity_id

_pdbx_branch_scheme.mon_id

_pdbx_branch_scheme.num

*_pdbx_branch_scheme.pdb_asym_id *

_pdbx_branch_scheme.pdb_mon_id

_pdbx_branch_scheme.pdb_seq_num

*_pdbx_branch_scheme.auth_asym_id *

_pdbx_branch_scheme.auth_mon_id

*_pdbx_branch_scheme.auth_seq_num*

_pdbx_branch_scheme.hetero

*J *4 NAG 1 *I* NAG 1 *A* NAG *1310* n

J 4 NAG 2 I NAG 2 A NAG 1311 n

K 4 NAG 1 J NAG 1 A NAG 1312 n

K 4 NAG 2 J NAG 2 A NAG 1313 n

L 4 NAG 1 K NAG 1 A NAG 1315 n

L 4 NAG 2 K NAG 2 A NAG 1316 n

M 4 NAG 1 M NAG 1 A NAG 1317 n

M 4 NAG 2 M NAG 2 A NAG 1318 n

N 5 NAG 1 N NAG 1 A NAG 1321 n

N 5 NAG 2 N NAG 2 A NAG 1322 n

N 5 BMA 3 N BMA 3 A BMA 1323 n

N 5 MAN 4 N MAN 4 A MAN 1325 n

N 5 MAN 5 N MAN 5 A MAN 1324 n

N 5 FUC 6 N FUC 6 A FUC 1320 n

O 4 NAG 1 O NAG 1 B NAG 1310 n

O 4 NAG 2 O NAG 2 B NAG 1311 n

P 4 NAG 1 P NAG 1 B NAG 1312 n

P 4 NAG 2 P NAG 2 B NAG 1313 n

Q 4 NAG 1 Q NAG 1 B NAG 1315 n

Q 4 NAG 2 Q NAG 2 B NAG 1316 n

R 4 NAG 1 R NAG 1 B NAG 1317 n

R 4 NAG 2 R NAG 2 B NAG 1318 n

S 5 NAG 1 S NAG 1 B NAG 1321 n

S 5 NAG 2 S NAG 2 B NAG 1322 n

S 5 BMA 3 S BMA 3 B BMA 1323 n

S 5 MAN 4 S MAN 4 B MAN 1325 n

S 5 MAN 5 S MAN 5 B MAN 1324 n

S 5 FUC 6 S FUC 6 B FUC 1320 n

...

#

As some users pointed out, single NAG could be just a part of the glycan 
that the author chose to build, as most natural N-glycans must have stem 
of a common core of 5 monosaccharides or its fucosylated version, such 
as those modeled in the PDB ID 6WPS. However, the PDB is a 3D-atomic 
coordinate archive in which the model coordinates are built based on 
supporting experimental data. Therefore, carbohydrates are described 
as-is in the modeled structures without reference to missing components 
of the presumed oligosaccharide sequence. If the author only builds a 
monosaccharide, then this monosaccharide is described as a non-polymer 
ligand.


Glycosylation annotation has been provided to facilitate searches of all 
glycosylation sites. A total of 45,000 glycosylation sites have been 
annotated in _struct_conn.pdbx_role in over 7500 PDB structures to 
identify all glycosylation sites and the monosaccharides bound at such 
sites. The annotation specifies the glycosylation sites, the 
monosaccharide identity and chain IDs in either PDB format or mmCIF 
format. In PDB ID 6WPS, a user can search N-Glycosylation in 
‘_struct_conn.pdbx_role’ and find 16 glycosylation sites between ASN and 
NAG at chain A alone.


The wwPDB encourages the community to use PDB/mmCIF format files rather 
than the frozen legacy PDB file format. The legacy format cannot support 
large structures. Currently, PDB format-files are not available for 
large structures that have either more than 62 chains or 99,999 atoms.  
In addition, the legacy format cannot support ligand ID codes beyond 
3-characters, which will be needed in the coming years.


We thank you again for your feedback. The wwPDB is committed to 
improving data representation in the PDB archive. Please do not hesitate 
to contact us at i...@wwpdb.org <mailto:i...@wwpdb.org>.



Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 12/4/20 3:15 PM, Marcin Wojdyr wrote:

On Fri, 4 Dec 2020 at 19:16, Dale Tronrud  wrote:

 Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is
exactly the problem.

It's not about "creating meaning" but about consistent naming. For humans.


"chain names" ( or "entity identifiers" if I
recall the mmCIF terminology correctly) are simply database "indexes".

No, entity is a somewhat different thing (m

[ccp4bb] Biocurator position opening at RCSB PDB/Rutgers University- Biological Structure Annotation Specialist

[Jasmine Young]

Analyze, curate, and validate macromolecular structures from the PDB 
community. Participate in exciting projects with significant impact on 
the scientific community.


RCSB PDB (RCSB.org),//the US data center for the global PDB archive, 
serves thousands of Data Depositors in the Americas and Oceania and 
makes 3D macromolecular structure data available at no charge and 
without usage restrictions to more than 1 million rcsb.org users 
worldwide.//


Deposition/Biocuration Services provide expert deposition, validation, 
biocuration, and remediation services to Data Depositors worldwide, 
ensure PDB data are Findable, Accessible, Interoperable, and Reusable 
(FAIR) by providing expert data curation which is critical for 
biological data resources, and develop and promote community-endorsed 
data standards for archiving and exchange of global structural biology data.


Roles:

·Analyze, curate, and validate macromolecular structures from the PDB 
community


·Participate in exciting projects with significant impact on the 
scientific community


·Communicate daily with members of the research community

·Participate in fun outreach activities


Why join us:

·Influence the development of structural biology as a field representing 
high scientific standards.


·Be part of a friendly and collaborative working environment with 
excellent professional development opportunities.


·At Rutgers, this academic position offers New Jersey state benefits and 
a faculty-level salary.


Knowledge and skills:

·Experience in structural biology with a PhD in a relevant field required

·Strong knowledge of small molecule chemistry or 3DEM preferred

·Experience in bioinformatics, cheminformatics, or computer scripting 
would be an advantage


The successful candidate should be self-motivated, pay close attention 
to details, possess strong interpersonal communication and writing 
skills, and have the ability to handle multiple projects.


Apply at Rutgers:

http://jobs.rutgers.edu/postings/106306



--


Regards,

Jasmine

===

JASMINE YOUNG, Ph.D.

Biocuration Team Lead, RCSB Protein Data Bank

Research Professor, Institute for Quantitative Biomedicine

Rutgers, The State University of New Jersey

174 Frelinghuysen Road, Piscataway NJ 08854

P: 848.445.4920 | E: jasmine.yo...@rcsb.org <mailto:jasmine.yo...@rcsb.org>

rcsb.org <http://rcsb.org/> | iqb.rutgers.edu 
<http://iqb.rutgers.edu/> | facebook 
<https://www.facebook.com/RCSBPDB> | twitter 
<https://twitter.com/buildmodels>


===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] One position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION & ANNOTATION SPECIALIST

[Jasmine Young]

*Curate, validate, and standardize macromolecular structures from the 
PDB community. Participate in exciting projects with significant impact 
on the scientific community.*


Data archives are critical to research and education. They provide safe 
and secure storage of valuable scientific data, and ensure that 
information is freely available to the world. Data curation is critical 
for these resources. In the case of PDB, data are carefully reviewed and 
annotated by wwPDB curators before public release. Expert curation of 
data coming into PDB is critical for ensuring findability, 
accessibility, interoperability, and reusability (FAIR). Biocurators 
communicate daily with members of the deposition community, and 
annotate, publicly release, and update entries in the PDB archive.


The RCSB PDB at Rutgers University in Piscataway, NJ has one position 
opening for a Biochemical Information & Annotation Specialist 
(Biocurator) to curate, validate, and standardize macromolecular 
structures for distribution in the PDB Core Archive.



This position offers the opportunity to participate in exciting projects 
with significant impact on the scientific community. The position is an 
academic position with state benefit. The salary is compatible with 
faculty level.


Knowledge and Skills:

 * PhD in Biological chemistry or chemistry is required
 * Background in 3DEM or crystallography has strong advantage
 * Experience with small molecules such as organometallic complexes is
   preferred
 * Knowledge of Linux computer systems and biological databases is
   preferred

The successful candidate should be self-motivated, pay close attention 
to detail, possess strong interpersonal, communication, and writing 
skills, with the ability to handle multiple projects, shifting 
priorities, while meeting deadlines.



Apply at Rutgers: http://jobs.rutgers.edu/postings/84303. 
<http://jobs.rutgers.edu/postings/84303>



--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Two position openings at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION & ANNOTATION SPECIALIST

[Jasmine Young]

*Curate, validate, and standardize macromolecular structures from the 
PDB community. Participate in exciting projects with significant impact 
on the scientific community.*


Data archives are critical to research and education. They provide safe 
and secure storage of valuable scientific data, and ensure that 
information is freely available to the world. Data curation is critical 
for these resources. In the case of PDB, data are carefully reviewed and 
annotated by wwPDB curators before public release. Expert curation of 
data coming into PDB is critical for ensuring findability, 
accessibility, interoperability, and reusability (FAIR). Biocurators 
communicate daily with members of the deposition community, and 
annotate, publicly release, and update entries in the PDB archive.


The RCSB PDB at Rutgers University in Piscataway, NJ has two openings 
for a Biochemical Information & Annotation Specialist (Biocurator) to 
curate, validate, and standardize macromolecular structures for 
distribution in the PDB Core Archive.



This position offers the opportunity to participate in exciting projects 
with significant impact on the scientific community. The position is an 
academic position with state benefit. The salary is compatible with 
faculty level.


Knowledge and Skills:

 * PhD in Biological chemistry or chemistry is required
 * Background in 3DEM or crystallography has strong advantage
 * Experience with small molecules such as organometallic complexes is
   preferred
 * Knowledge of Linux computer systems and biological databases is
   preferred

The successful candidate should be self-motivated, pay close attention 
to detail, possess strong interpersonal, communication, and writing 
skills, with the ability to handle multiple projects, shifting 
priorities, while meeting deadlines. This academic position has state 
benefits and a faculty-level salary.



Apply at Rutgers: http://jobs.rutgers.edu/postings/84303. 
<http://jobs.rutgers.edu/postings/84303>




--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION & ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (RCSB PDB, rcsb.org ) is a 
publicly accessible information portal for researchers and students 
interested in structural biology. At its center is the PDB Core Archive 
– the single global repository for the 3-dimensional structure data of 
biological macromolecules. These structures hold significant promise for 
the pharmaceutical and biotechnology industries in the search for new 
drugs and in efforts to understand human disease.


The primary mission of the RCSB PDB is to provide accurate, 
well-annotated data in the most timely and efficient way to facilitate 
new discoveries and scientific advances. The RCSB PDB processes, stores, 
and disseminates these important data, and develops the software tools 
needed to assist users in depositing (in collaboration with worldwide 
PDB partners) and accessing structural information.


The RCSB PDB at Rutgers University in Piscataway, NJ has an opening for 
a Biochemical Information & Annotation Specialist (Biocurator) to 
curate, validate, and standardize macromolecular structures for 
distribution in the PDB Core Archive. Data curation is critical for 
these resources. In the case of PDB, data


are carefully reviewed and annotated by wwPDB curators before 
publicrelease. Expert curation of data coming into PDB is critical for 
ensuring findability, accessibility, interoperability, and reusability 
(FAIR). Biocurators communicate daily with members of the deposition 
community, and annotate, publicly release, and update entries in the PDB 
Core Archive.


The position is an academic position with state benefit. The salary is 
compatible with faculty level.


A background in cryo-electron microscopy or small molecule 
crystallography or macromolecular crystallography is a strong advantage. 
Biological chemistry in PhD is required. Experience with metalloprotein, 
small molecules, linux computer systems, biological databases is 
preferred. The successful candidate should be self-motivated, pay close 
attention to detail, possess strong interpersonal, communication, and 
writing skills with the ability to handle multiple projects, shift 
priority, and meet deadlines.


This position offers the opportunity to participate in exciting projects 
with significant impact on the scientific community.


Please apply this job at http://jobs.rutgers.edu/postings/84303. 








To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Better Management of PDB Archive with File Versioning and Revision History

[Jasmine Young]

As announced 
<https://www.wwpdb.org/news/news?year=2017#5910c8d8d3b1d333029d4ea8> on 
May 17, 2017, wwPDB will introduce a file versioning system to retain 
depositor-initiated updates of previously released coordinate entries. A 
new FTP repository will host versioned files. Versions will be separated 
into major and minor updates. 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 
latest major versions of each PDB structure will be retained in the new 
FTP archive.


wwPDB will deliver versioned files in two phases:

 * Phase 1 (October 2017), we will release the new versioned FTP
   archive at ftp://ftp-version.wwpdb.org for structural model files in
   PDBx/mmCIF and PDBML formats.
 * Phase 2 will be released in 2018 and will support
   depositor-initiated updates of coordinates in PDBx/mmCIF and PDBML
   formats.

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


__v-..

The familiar 4 character PDB accession code will be extended to 8 
characters and will include the prefix “pdb”. Thus PDB accession code 
for entry 1abc would become pdb_1abc.


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 zipped 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 will be stored in single 
directory following a 2 character hash from the penultimate two 
characters of the PDB code:


../pub/pdb_versioned/data/entries///

For example, major version 1 with minor version 2 file for entry 1ABC 
would have the following path:


../pub/pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc_xyz_v1-2.cif.gz

Different views of the repository will be provided for the most common 
use cases as a convenience for repository users. For 2017 phase 1, views 
by content type and format similar to the current repository will be 
introduced. All latest major versions are included.


../pub/pdb_versioned/views/

For example, the coordinate files in mmCIF format for entry 1ABC will be 
made available at


../pub/pdb_versioned/views/coordinates/mmcif/ab/pdb_1abc/pdb_1abc_xyz_v1-2.cif.gz

../pub/pdb_versioned/views/coordinates/mmcif/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 contain only the latest version for every 
entry.



<https://www.wwpdb.org/news/news?year=2017#top>

--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

Re: [ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

[Jasmine Young]

Hi Ed,

The PDB accession code will be based on the primary data stored in the 
PDB.  Therefore depositors will need to make a new deposition with new 
PDB accession code issued if the atomic coordinates are modified using 
newly processed intensities from the original diffraction images.


More details on the procedure will be made available at a later date.


Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 5/17/17 12:11 PM, Edward A. Berry wrote:

Couple of wuestions:
What is the procedure for updating an entry? Start a new submission, 
or mail revised coordinates along with an explanation of changes to 
deposit@rcsb?


"unchanged experimental data" - does this mean the exact same 
structure factors, or will newly reduced data from the same original 
diffraction images be acceptable?


Thanks,
Ed

On 05/17/2017 09:28 AM, Jasmine Young wrote:
*Use CAUTION opening attachments or clicking on links in emails - IMT 
Help Desk, 4-4115*




The wwPDB is planning to introduce in 2017 a new procedure for the 
management by the Depositor of Record (where the Depositor of Record 
is defined as the Principal Investigator for the entry) of 
substantial revisions to previously released PDB archival entries.


At present, revised atomic coordinates for an existing released PDB 
entry are assigned a new accession code, and the prior entry is 
obsoleted. This long-standing wwPDB policy had the unintended 
consequence of breaking connections with publications and usage of 
the prior set of atomic coordinates, resulting in a non-trivial 
barrier to submission of atomic coordinate revisions by our 
Depositors of Record.


The wwPDB is introducing a file versioning system that allows 
Depositors of Record to update their own previously released entries. 
Please note, in the first phase, file versioning will be applied to 
the atomic coordinates refined versus unchanged experimental data.


Version numbers of each PDB archive entry will be designated using a 
#-# identifier. The first digit specifies the major version, and the 
second designates the minor version. The Structure of Record (i.e., 
the initial set of released atomic coordinates) is designated as 
Version 1-0. Thereafter, the major version digit is incremented with 
each substantial revision of a given entry (e.g., Version 2-0, when 
the atomic coordinates are replaced for the first time by the 
Depositor of Record). “Major version changes” are defined as updates 
to the atomic coordinates, polymer sequence(s), and/or chemical 
identify of a ligand. All other changes are defined as “minor 
changes”. When a major change is made, the minor version number is 
reset to 0 (e.g., 1-0 to 1-1 to 2-0). For the avoidance of doubt, the 
wwPDB will retain all major versions with the latest minor versions 
of an entry within the PDB archive.


Current wwPDB policies governing the deposition of independently 
refined structures based on the data generated by a research group or 
laboratory separate from that of the Depositor of Record remain 
unchanged. Versioning of atomic coordinates will be strictly limited 
to substitutions made by the Depositor of Record.


Upon introduction of the file versioning system, the wwPDB will 
revise each PDB accession code by extending its length and prepending 
“PDB” (e.g., "1abc" will become "pdb_1abc"). This process will 
enable text mining detection of PDB entries in the published 
literature and allow for more informative and transparent delivery of 
revised data files. For example, the atomic coordinates for the 
second major version of PDB entry 1abc would have the following form 
under the new file-naming schema:


pdb_1abc_xyz_v2-0.cif.gz

The wwPDB is mindful of the importance of continuity in providing 
services and supporting User activities. For as long as practicable, 
the wwPDB will continue assigning PDB codes that can be truncated 
losslessly to the current four-character style. In the same spirit, 
initial implementation of entry file versioning will appear in a new, 
parallel branch of the PDB archive FTP tree. More details on the new 
FTP tree organization and accessibility of version information will 
be forthcoming. 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 contain the latest version in the 
corresponding versioned archive.



<http://www.wwpdb.org/news/news?year=2017#top>

--
Regards,

Jasmine

=======
Jasmine Young, Ph.D

[ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

[Jasmine Young]

The wwPDB is planning to introduce in 2017 a new procedure for the 
management by the Depositor of Record (where the Depositor of Record is 
defined as the Principal Investigator for the entry) of substantial 
revisions to previously released PDB archival entries.


At present, revised atomic coordinates for an existing released PDB 
entry are assigned a new accession code, and the prior entry is 
obsoleted. This long-standing wwPDB policy had the unintended 
consequence of breaking connections with publications and usage of the 
prior set of atomic coordinates, resulting in a non-trivial barrier to 
submission of atomic coordinate revisions by our Depositors of Record.


The wwPDB is introducing a file versioning system that allows Depositors 
of Record to update their own previously released entries. Please note, 
in the first phase, file versioning will be applied to the atomic 
coordinates refined versus unchanged experimental data.


Version numbers of each PDB archive entry will be designated using a #-# 
identifier. The first digit specifies the major version, and the second 
designates the minor version. The Structure of Record (i.e., the initial 
set of released atomic coordinates) is designated as Version 1-0. 
Thereafter, the major version digit is incremented with each substantial 
revision of a given entry (e.g., Version 2-0, when the atomic 
coordinates are replaced for the first time by the Depositor of Record). 
“Major version changes” are defined as updates to the atomic 
coordinates, polymer sequence(s), and/or chemical identify of a ligand. 
All other changes are defined as “minor changes”. When a major change is 
made, the minor version number is reset to 0 (e.g., 1-0 to 1-1 to 2-0). 
For the avoidance of doubt, the wwPDB will retain all major versions 
with the latest minor versions of an entry within the PDB archive.


Current wwPDB policies governing the deposition of independently refined 
structures based on the data generated by a research group or laboratory 
separate from that of the Depositor of Record remain unchanged. 
Versioning of atomic coordinates will be strictly limited to 
substitutions made by the Depositor of Record.


Upon introduction of the file versioning system, the wwPDB will revise 
each PDB accession code by extending its length and prepending “PDB” 
(e.g., "1abc" will become "pdb_1abc"). This process will enable text 
mining detection of PDB entries in the published literature and allow 
for more informative and transparent delivery of revised data files. For 
example, the atomic coordinates for the second major version of PDB 
entry 1abc would have the following form under the new file-naming schema:


pdb_1abc_xyz_v2-0.cif.gz

The wwPDB is mindful of the importance of continuity in providing 
services and supporting User activities. For as long as practicable, the 
wwPDB will continue assigning PDB codes that can be truncated losslessly 
to the current four-character style. In the same spirit, initial 
implementation of entry file versioning will appear in a new, parallel 
branch of the PDB archive FTP tree. More details on the new FTP tree 
organization and accessibility of version information will be 
forthcoming. 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 contain the latest version in the 
corresponding versioned archive.



<http://www.wwpdb.org/news/news?year=2017#top>

--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing

[Jasmine Young]

On July 12, 2017, the wwPDB partners plan to update the PDB FTP archive 
with PDB structure entry files conforming to V5.0 of the PDBx/mmCIF 
dictionary 
<http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/>, which 
already supports the global wwPDB system for Deposition, Biocuration, 
and Validation of PDB data - OneDep 
<https://www.wwpdb.org/deposition/system-information>.


In preparation for this update, to allow the community ample time to 
test the planned update and to provide feedback, the wwPDB is now 
delivering PDBx/mmCIF and XML structure entry files for all entries in 
the PDB archive conforming to the new data standards via a new FTP 
repository (ftp://ftp-beta.wwpdb.org/). This collection of test files 
will be updated in concert with regular weekly updates of the PDB archive.


Complete lists of changes can be found at the wwPDB website 
(https://www.wwpdb.org/documentation/remediation).


The wwPDB strongly encourages the community to review and test the 
updated files.


Users should report V5.0 data issues to deposit-h...@mail.wwpdb.org 
<mailto:deposit-h...@mail.wwpdb.org>


We will attempt to address the reported issues incrementally as User 
feedback is received in advance of the rollout on July 12, 2017.


Other derived data and experimental data files of ftp-beta tree will be 
delivered incrementally to the ftp-beta tree between May 3 and July 12, 
2017.


The test FTP area (ftp://ftp.wwpdb.org/pub/pdb/test_data/EM/) containing 
previously updated 3DEM model files (previously made available in 
December 2016) is to be retired effective May 3 2017.



<https://www.wwpdb.org/news/news?year=2017#top>

--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] Updated Validation Reports for Archived PDB Structures Now Available

[Jasmine Young]

The wwPDB partners are pleased to announce that updated validation 
reports for all X-ray, NMR, and 3DEM structures deposited in the PDB 
archive are now available on March 15, 2017.


The updates include new percentile statistics reflecting the state of 
the PDB archive on December 31th 2016 and updated versions of the Mogul 
software (2017) and CSD archive (as538be).


The updated reports are accessible from the following FTP sites:

 * ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)
 * ftp://ftp.rcsb.org/pub/pdb/validation_reports/ (RCSB PDB)
 * ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)
 * ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj)

A copy of the previous version is archived at RCSB PDB 
<ftp://snapshots.wwpdb.org/20170308/pub/> and PDBj 
<ftp://snapshots.pdbj.org/20170308/pub/>.


These updated wwPDB validation reports provide an assessment of 
structure quality using widely accepted standards and criteria, 
recommended by community experts serving in the Validation Task Force 
<https://www.wwpdb.org/task/validation-task-forces>. The wwPDB partners 
strongly encourage journal editors and referees to request them from 
authors as part of the manuscript submission and review process. The 
reports are date-stamped and display the wwPDB logo, and contain the 
same information, regardless of which wwPDB site processed the entry. 
Provision of wwPDB validation reports is 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/ as part of their 
manuscript-submission process.


Validation reports are also provided to depositors through OneDep - the 
wwPDB portal for validation, deposition and biocuration of structure 
data. The wwPDB partners encourage the use of the stand-alone validation 
server <http://validate.wwpdb.org/> and the webservice API 
<https://www.wwpdb.org/validation/onedep-validation-web-service-interface> 
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 
X-ray <https://www.wwpdb.org/task/xray>, NMR 
<https://www.wwpdb.org/task/nmr>, EM <https://www.wwpdb.org/task/em>, 
and on ligand validation, and as we collect feedback from depositors and 
users.


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


Your feedback, comments, and questions are welcome at 
validat...@mail.wwpdb.org <mailto:validat...@mail.wwpdb.org>.



--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] The paper describing wwPDB OneDep system is now available.

[Jasmine Young]

The paper 
<http://www.cell.com/structure/fulltext/S0969-2126%2817%2930004-7> 
describing wwPDB OneDep system <http://deposit.wwpdb.org/> is now 
available. The wwPDB has deployed a unified system for deposition, 
biocuration, and validation of macromolecular structures globally across 
all wwPDB, EMDB, and BMRB deposition sites to meet the evolving 
requirements of the scientific community to archive structural data over 
the coming decades.


The OneDep system provides a user-friendly deposition interface and 
improved structure validation <http://validate.wwpdb.org/> with the 
benefit of recommendations from expert task forces 
<http://wwpdb.org/task/validation-task-forces> representing the 
respective methodological communities. The processing efficiency in 
biocuration is improved as OneDep supports a more automated workflow .


As Milka Kostic, the Senior Editor at */Structure/* and */Cell Chemical 
Biology/* described, OneDep is a step in the right direction 
<http://crosstalk.cell.com/blog/onedep-is-a-step-in-the-right-direction> 
and offers a single point of entry into the atomic coordinate deposition 
process, as well as improving processes of structure validation and data 
biocuration.



--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] 2016 Remediation of 3DEM Entries in the PDB archive

[Jasmine Young]

The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project 
<https://www.ncbi.nlm.nih.gov/pubmed/26578576> have collaborated to 
update the experimental methods descriptions of all electron microscopy 
and electron crystallography-derived structures in the PDB archive. With 
this work now completed, all 3DEM-derived entries have better-organized 
content and conform to the revised data model developed by the 
EMDataBank team for use within the wwPDB OneDep System 
<http://wwpdb.org/deposition/system-information>. The OneDep System has 
supported deposition, annotation, and validation of 3DEM structures and 
fully integrates deposition of 3DEM maps and model coordinates since 
January 2016.


Examples of 3DEM model files (both remediated and from the OneDep 
system) are provided in a new wwPDB ftp directory 
(ftp://ftp.wwpdb.org/pub/pdb/test_data/EM/). A data-item level 
description of the changes made during remediation is provided here 
<http://cdn.wwpdb.org/wwpdb/docs/documentation/remediation/summary-changes.xlsx>. 
3DEM terms in the updated PDBx/mmCIF dictionary can be reviewed here 
<http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v5_rc.dic/Groups/em_group.html>.


Files in the current PDB ftp archive will be replaced with new files 
corresponding to the updated PDBx/mmCIF dictionary in 2017. Users are 
encouraged to review and test the example data files.


We welcome your feedback. Please send any comments or questions to 
deposit-h...@mail.wwpdb.org.




--
Regards,

Jasmine

=======
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (www.rcsb.org) is a publicly accessible information portal for 
researchers and students interested in structural biology. At its center is the PDB archive-the sole 
international repository for the 3-dimensional structure data of biological macromolecules. These 
structures hold significant promise for the pharmaceutical and biotechnology industries in the 
search for new drugs and in efforts to understand the mysteries of human disease.


The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most 
timely and efficient way possible to facilitate new discoveries and scientific advances. The RCSB 
PDB processes, stores, and disseminates these important data, and develops the software tools needed 
to assist users in depositing and accessing structural information.


The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has an opening for a 
Biochemical Information  Annotation Specialist to curate and standardize macromolecular structures 
for distribution in the PDB archive. Annotation Specialists validate, annotate, and release 
structural entries in PDB archive. Annotation Specialists also communicate daily with members of the 
deposition community. The position is an academic position with state benefit. The salary is 
compatible with faculty level.


A background in macromolecular crystallography or small molecule crystallography is a strong 
advantage. Biological chemistry background (PhD, MS) is required. Experience with Linux computer 
systems and biological databases is preferred. The successful candidate should be self-motivated, 
pay close attention to details, possess strong written and oral communication skills, and meet 
deadlines.


This position offers the opportunity to participate in an exciting project with significant 
impact on the scientific community.


Please send resume (PDF preferred) to Dr. Jasmine Young at 
pdbj...@rcsb.rutgers.edu.


--

Jasmine Young, Ph.D.
RCSB Protein Data Bank
Assistant Research Professor
Lead biocurator
Center for Integrative Proteomics Research
Rutgers The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:  jas...@rcsb.rutgers.edu
Phone:  (848)-445-0103 ext 4920
Fax:(732)-445-4320

[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for 
researchers and students interested in structural biology. At its center is the PDB archive – the 
sole international repository for the 3-dimensional structure data of biological macromolecules. 
These structures hold significant promise for the pharmaceutical and biotechnology industries in the 
search for new drugs and in efforts to understand the mysteries of human disease.


The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most timely 
and efficient way possible to facilitate new discoveries and scientific advances. The RCSB PDB 
processes, stores, and disseminates these important data, and develops the software tools needed to 
assist users in depositing and accessing structural information.


The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has one opening for a Biochemical 
Information  Annotation Specialist to curate and standardize macromolecular structures for 
distribution in the PDB archive. The annotation specialists validate, annotate, and release 
structural entries in PDB archive. The annotation specialists also communicate daily with members of 
the deposition community. The position is an academic position with state benefit.

The salary is compatible with faculty level.

A background in macromolecular crystallography or small molecule crystallography is a strong 
advantage. Biological chemistry (PhD, MS) is required. Experience with linux computer systems, 
biological databases is preferred. The successful candidate should be self-motivated, pay close

attention to details, possess strong written and oral communication skills, and 
meet deadlines.

This position offers the opportunity to participate in an exciting project with significant impact 
on the scientific community.


Please send resume (pdf preferred) to Dr. Jasmine Young at 
pdbj...@rcsb.rutgers.edu.


--

Jasmine Young, Ph.D.
RCSB Protein Data Bank
Assistant Research Professor
Lead biocurator
Center for Integrative Proteomics Research
Rutgers The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:  jas...@rcsb.rutgers.edu
Phone:  (848)-445-0103 ext 4920
Fax:(732)-445-4320

Re: [ccp4bb] pdb_extact and refmac5.6

[Jasmine Young]

Hello,

We are currently in the final stages of updating the standalone version of 
pdb_extract.

In the meantime, we encourage users to try the web server version of the program at 
http://pdb-extract.rcsb.org/


The PDB_extract will:
# provide you with an author information form, which can be saved/updated for 
multiple related entries
# assemble coordinate and log files pertaining to your specific experimental 
methods
# allow you to fix the primary sequence of your protein/nucleotide chains to account for 
unresolved residues
# output the coordinate (and structure factor files, if applicable) in mmCIF format for Validation 
and for deposition at RCSB ADIT or PDBj ADIT.


If the web version produces similar errors, please email the log file to use at 
depo...@deposit.rcsb.org and we will look into it.




Sincerely,

Jasmine



Jan Abendroth wrote:

Hi all,
we typically use pdb_extract to generate pdb files with a good header.
There seems to be an issue with logfiles from refmac5.6.0117, 
distributed with the current ccp4 version, and pdb_extract.


pdb_extract version-3.006 is distributed with ccp4-6.2.0. While reading 
the refmac log file, pdb_extract chokes with a segmentation fault. When 
run without reading in the refmac log file, the program complains about 
the following missing link, both in the linux and osx distribution of ccp4.


Can not open file 
(/usr/local/ccp4/ccp4-6.2.0/ccp4-6.2.0//src/harvest_app_/pdb_extract/pdb-extract-data/mmcif_pdbx_2.items) 
in get_lines_from_file


pdb_extract version-3.010, as downloaded form the rcsb webpage also 
chokes on the refmac5 logfile with a segmentation fault.


Any ideas how to treat the new refmac log files in pdb_extract?

Thanks a lot.
Jan


--
Jan Abendroth
Emerald Biostructures
Seattle / Bainbridge Island, WA, USA
home: Jan.Abendroth_at_gmail.com http://Jan.Abendroth_at_gmail.com
work: JAbendroth_at_embios.com
http://www.emeraldbiostructures.com



--

Jasmine Young, Ph.D.
RCSB Protein Data Bank
Assistant Research Professor
Lead biocurator
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087

Email:  jas...@rcsb.rutgers.edu
Phone:  (732)-445-0103
Fax:(732)-445-4320

[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for 
researchers and students interested in structural biology. At its center is the PDB archive – the 
sole international repository for the 3-dimensional structure data of biological macromolecules. 
These structures hold significant promise for the pharmaceutical and biotechnology industries in the 
search for new drugs and in efforts to understand the mysteries of human disease.


The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most timely 
and efficient way possible to facilitate new discoveries and scientific advances. The RCSB 
processes, stores, and disseminates these important data, and develops the software tools needed to 
assist users in depositing and accessing structural information.


The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has one opening for a Biochemical 
Information  Annotation Specialist to curate and standardize macromolecular structures for 
distribution in the PDB archive. The annotation specialists validate, annotate, and release 
structural entries in PDB archive. The annotation specialists also communicate daily with members of 
the deposition community. The position is an academic position with state benefit.

The salary is compatible with faculty level.

A background in macromolecular crystallography or small molecule crystallography is a strong 
advantage. Biological chemistry (PhD, MS) is required. Experience with linux computer systems, 
biological databases is preferred. The successful candidate should be self-motivated, pay close

attention to detail, possess strong written and oral communication skills, and 
meet deadlines.

This position offer the opportunity to participate in an exciting project with significant impact on 
the scientific community.


Please send resume (pdf preferred) to Dr. Jasmine Young at 
pdbj...@rcsb.rutgers.edu.

[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for 
researchers and students interested in structural biology. At its center is the PDB archive – the 
sole international repository for the 3-dimensional structure data of biological macromolecules. 
These structures hold significant promise for the pharmaceutical and biotechnology industries in the 
search for new drugs and in efforts to understand the mysteries of human disease.


The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most timely 
and efficient way possible to facilitate new discoveries and scientific advances. The RCSB 
processes, stores, and disseminates these important data, and develops the software tools needed to 
assist users in depositing and accessing structural information.


The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has one opening for a Biochemical 
Information  Annotation Specialist to curate and standardize macromolecular structures for 
distribution in the PDB archive. The annotation specialists validate, annotate, and release 
structural entries in PDB archive. The annotation specialists also communicate daily with members of 
the deposition community. The position is an academic position with state benefit.

The salary is compatible with faculty level.

A background in macromolecular crystallography or small molecule crystallography is a strong 
advantage. Biological chemistry (PhD, MS) is required. Experience with linux computer systems, 
biological databases is preferred. The successful candidate should be self-motivated, pay close

attention to detail, possess strong written and oral communication skills, and 
meet deadlines.

This position offer the opportunity to participate in an exciting project with significant impact on 
the scientific community.


Please send resume (pdf preferred) to Dr. Jasmine Young at 
pdbj...@rcsb.rutgers.edu.


--

Jasmine Young, Ph.D.
RCSB Protein Data Bank
Assistant Research Professor
Lead biocurator
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087

Email:  jas...@rcsb.rutgers.edu
Phone:  (732)-445-5497
Fax:(732)-445-4320

Re: [ccp4bb] PDB Validation Report

[Jasmine Young]

Dear Katja,

You can find below information from PDB Format Guide, 
http://www.wwpdb.org/documentation/format32/remarks2.html#REMARK%20500.
The improper CA-C-CB-N angles for chiral centers are calculated and are 
listed in REMARK 500 of PDB file.

It is defined below with 10 degree allowed deviations.

+35 for L amino acids
-35 for D amino acids

* +25 to +45 degree range is defined as sp3, L.
If D is expected, it gives WRONG HAND in the details. If the 
calculated value is positive and outside this range, it gives OUTSIDE 
RANGE in the details.

* -10 to +10 degree range is defined as sp2, planar.
If it is expected to be sp2 and the value is outside this range, it 
gives EXPECTING PLANAR in the details. If it is expected to be sp3 and 
the value is within this range, it gives EXPECTING SP3 in the details.

* -45 to -25 degree range is defined as sp3, D.
If L is expected, it gives WRONG HAND in the details. If the 
calculated value is negative and outside this range, it gives OUTSIDE 
RANGE in the details.



Hope this information help.


Jasmine


From: Katja Schleider katjaschlei...@yahoo.de
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB Validation Report

Dear all,

I just finished my first protein structure. More or less. I'm using 
right now the pdb
validation server to check the data and the data look quite well. The 
only point

irretating is following line in the Adit Validation Report:

The following residues have unexpected configuration of the
chiral center using C(i) - N(i) - Ca(i) - Cb(i) chirality.

Residue Chain Sequence Improper Details
LYS A 470 22.18 Expecting L Found L OUTSIDE RANGE
I am not sure what this means and what I should do. What is outside 
the L range? I would be thankful for any advice.


Thanks,

Katja





--
===
Jasmine Young, Ph.D.
RCSB Protein Data Bank
Assistant Research Professor
Lead biocurator
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087 


Email:+jas...@rcsb.rutgers.edu
Phone:+(732)445-0103+ext 231 Fax: (732)445-4320
===

[ccp4bb] Positions available at RCSB PDB- BIOCHEMICAL INFORMATION ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible 
information portal for researchers and students interested in structural 
biology. At its center is the PDB archive – the sole international 
repository for the 3-dimensional structure data of biological 
macromolecules. These structures hold significant promise for the 
pharmaceutical and biotechnology industries in the search for new drugs 
and in efforts to understand the mysteries of human disease.


The primary mission of the RCSB PDB is to provide accurate, 
well-annotated data in the most timely and efficient way possible to 
facilitate new discoveries and scientific advances. The RCSB processes, 
stores, and disseminates these important data, and develops the software 
tools needed to assist users in depositing and accessing structural 
information.


The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has 
two openings for a Biochemical Information  Annotation Specialists to 
curate and standardize macromolecular structures for distribution in the 
PDB archive. The annotation specialists validate, annotate, and release 
structural entries in PDB archive. The annotation specialists also 
communicate daily with members of the deposition community. The position 
is an academic position with state benefit. The salary is compatible 
with faculty level.


A background in macromolecular crystallography or small molecule 
crystallography or cryo-electron microscopy is a strong advantage. 
Biological chemistry (PhD, MS) is required. Experience with linux 
computer systems, biological databases is preferred. The successful 
candidate should be self-motivated, pay close attention to detail, 
possess strong written and oral communication skills, and meet deadlines.


These positions offer the opportunity to participate in an exciting 
project with significant impact on the scientific community.


Please send resume (pdf preferred) to Dr. Helen M. Berman at 
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]

[ccp4bb] Seeking for Scientific Lead for the RCSB Protein Data Bank (PDB) Site at the University of California in San Diego (UCSD)

[Jasmine Young]

The RCSB Protein Data Bank (http://www.pdb.org), is looking for a 
Scientific Lead to assist in the advancement of the data dissemination 
strategies and delivery of important data viewing tools.  The incumbent 
will function as the Scientific Lead for the RCSB Protein Data Bank 
(PDB) Site at the University of California in San Diego (UCSD).   The 
incumbent will work with the PDB Director, Co-Director and scientific 
staff at both Rutgers and San Diego to define the scientific objectives 
for the RCSB Web Site, provide functional requirements and participate 
in the development of tools to enhance the analysis tools offered by the 
PDB to the scientific community.  The incumbent will have deep domain 
knowledge in structural biology, computational biology or related 
discipline as well as experience in programming scientific 
applications.  He/She will be skilled at working with scientists from 
diverse disciplines as well as IT development staff.  The over arching 
goal for this individual will be to provide the PDB user community with 
relevant and creative tools with which to access and analyze the wealth 
of the PDB content to enhance their own research efforts.   A specific 
long term goal is to create a series of domain specific interfaces to 
PDB data that permit both simple and complex queries to be addressed by 
a variety of audiences ranging from K12 to advanced researchers from the 
life and medical sciences.


Send resume and cover letter to: [EMAIL PROTECTED]

[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (_http://www.pdb.org http://www.pdb.org/_) 
is a publicly accessible information portal for researchers and students 
interested in structural biology. At its center is the PDB archive -- 
the sole international repository for the 3-dimensional structure data 
of biological macromolecules. These structures hold significant promise 
for the pharmaceutical and biotechnology industries in the search for 
new drugs and in efforts to understand the mysteries of human disease


The primary mission of the RCSB PDB is to provide accurate, 
well-annotated data in the most timely and efficient way possible to 
facilitate new discoveries and scientific advances. The RCSB processes, 
stores, and disseminates these important data, and develops the software 
tools needed to assist users in depositing and accessing structural 
information


The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has 
an opening for a Biochemical Information  Annotation Specialist to 
curate and standardize macromolecular structures for distribution in the 
PDB archive. The annotation specialist communicates daily with members 
of the deposition community, and annotates, releases, and updates 
entries in the PDB archive. BLAST, PubMed, and other tools are used for 
the annotation process performed on a linux box


A background in cryo-electron microscopy is a strong advantage. 
Biological chemistry (PhD, MS, BS or BA) is required. Experience with 
linux computer systems, biological databases is preferred. The 
successful candidate should be self-motivated, pay close attention to 
detail, possess strong written and oral communication skills, and meet 
deadlines


This position offers the opportunity to participate in an exciting 
project with significant impact on the scientific community


Please send resume (pdf preferred) to Dr. Helen M. Berman at 
[EMAIL PROTECTED] 
http://aaas.sciencecareers.org/texis/apply?id=4550f6e14a09a20lookid=aaas[EMAIL PROTECTED]_