PDB Newsletter
Number 1 -- January 1999 -- RCSB
Published quarterly by the Research Collaboratory for Structural
Bioinformatics
This newsletter is available on the Web in HTML and PDF formats at
http://www.rcsb.org/pdb/newsletter/
SNAPSHOT: January 1999
9176 Released atomic coordinate entries
Molecule Type
8143 proteins, peptides, and viruses
381 protein/nucleic acid complexes
643 nucleic acids
12 carbohydrates
Experimental Technique
206 theoretical modeling
1452 NMR
7521 diffraction and other
2424 structure factor files
522 NMR restraint files
TABLE OF CONTENTS
- Welcome from Helen M. Berman
- The Members of the RCSB
- Current and Future Status of the PDB
- mmCIF and PDB formats in the RCSB PDB
- RCSB PDB Meetings and Presentations
- New PDB Web Tools
- The PDB E-Mail Discussion Group
- Linking to the PDB through your Browser
- OMG Requests User Input Regarding CORBA Protocol Specification
for Macromolecular Structure
- Statement of Support
- PDB Staff
-----------------------------------------
WELCOME FROM HELEN M. BERMAN
Welcome to the first newsletter of the Research Collaboratory for
Structural Bioinformatics (RCSB) for the Protein Data Bank (PDB). As you
all know, the management of the PDB has changed from Brookhaven National
Laboratory (BNL) to the RCSB. This change in management will take place
during a transition period that will end October 31, 1999. In this
newsletter, we introduce ourselves, our plans for the transition, and our
plans for the future.
We have received a variety of responses to this news. Thanks to all of you
who have sent your support. We are aware that there are some concerns over
this change in management; if you are interested in a particular area that
is not addressed in this newsletter or on our Web site
(http://www.rcsb.org/), please let us know by sending e-mail to
info@rcsb.org.
We are looking forward to introducing the RCSB system and its many new
features. We are particularly excited about a higher, faster throughput of
deposited data; a greater number of query capabilities, including more
complex and more accurate queries; a uniform archive; dynamic cross-links
to other databases; and the availability of structure and sequence
neighboring. The PDB data will be stored and mirrored at all three RCSB
sites. The RCSB has entered several different collaborations and will be
highlighting these projects and other developments in newsletters to come.
Helen M. Berman
-----------------------------------------
MEMBERS OF THE RCSB
The Research Collaboratory for Structural Bioinformatics (RCSB) is a
non-profit consortium dedicated to improving our understanding of the
function of biological systems through an understanding of 3-D biological
macromolecular structure.
The PDB is managed by an RCSB Project Team directed by Dr. Helen M. Berman.
The Project Team consists of:
Helen M. Berman, a structural biologist, is a Professor II in the
Department of Chemistry and a member of the Waksman Institute at Rutgers,
the State University of New Jersey. Dr. Berman is the Director Designee of
the Protein Data Bank. She has founded and directs the Nucleic Acid
Database Project and has been a leader in the national and international
mmCIF effort. She is the chair of the International Union of
Crystallography Database Committee. Dr. Berman was President of the
American Crystallographic Association (ACA) and has served on
numerous advisory boards. Dr. Berman was one of the founders of the PDB.
John Westbrook, a bioinformaticist, is a Research Associate Professor in
the Department of Chemistry at Rutgers, the State University of New Jersey.
Dr. Westbrook is the principal architect of the Nucleic Acid Database. He
is the author of the Dictionary Definition Language used by mmCIF and is
one of the two Technical Editors for the mmCIF Dictionary. Dr. Westbrook is
also a key member of the imgCIF project, which is creating an exchange
format for diffraction data. Dr. Westbrook was formerly the Director of
Computational Chemistry at Rutgers.
Gary Gilliland, a structural biologist, is the Chief of the Biotechnology
Division of the Chemical Science and Technology Laboratory of the National
Institute of Science and Technology (NIST) and an Adjunct Professor of the
University of Maryland Biotechnology Institute at the Center for Advanced
Research in Biotechnology (CARB). Dr. Gilliland founded the Biological
Macromolecular Crystallization Database (BMCD) and, for the past 10 years,
has organized and been an instructor for the macromolecular crystallography
course offered by Cold Spring Harbor Laboratory. He is a former Associate
Director of CARB.
Phoebe Fagan, a scientific database developer, has extensive experience in
related activities carried out during her tenure in NIST's Standard
Reference Data Program. Ms. Fagan is a program manager and has experience
in managing database review and quality control. Previously, Fagan headed
the database development group within NIST Standard Reference Data Program
and initiated its archive.
Peter Arzberger, a computational biologist, is Executive Director of the
National Partnership for Advanced Computational Infrastructure (NPACI),
which involves the coordination of software development and implementation
activities among 46 institutions via 10 applications and technology thrust
areas. Dr. Arzberger was formerly Deputy NSF HPCC Coordinator and Program
Director of the Computational Biology and of the Statistics and Probability
programs.
Phil Bourne, a structural biologist, is a Senior Principle Scientist at the
San Diego Supercomputer Center and an Adjunct Professor in the Department
of Pharmacology, UCSD and the Burnham Institute. He has more than 20 years
experience as a small molecule and macromolecular crystallographer and, in
the last five years, in bioinformatics. He is chairman of the International
Union of Crystallography Computing Commission and the American
Crystallography Association Data and Computing Committee. He oversees a
major molecular sciences project for NPACI, which is charged with providing
the capability to query biological data.
-----------------------------------------
CURRENT AND FUTURE STATUS OF THE PDB
Data Processing
Query
Distribution
STATUS OF DATA PROCESSING DURING TRANSITION PERIOD
On January 27, 1999, the RCSB became responsible for the processing of all
data received by the PDB. Brookhaven National Laboratory (BNL) will be
responsible for processing the files received prior to January 27, 1999.
For now, the process of depositing data will not change. Crystal structures
of Proteins and all NMR structures should be deposited using either AutoDep
or the PDB Deposition Form, which are available at http://www.pdb.bnl.gov/
and http://www2.ebi.ac.uk/pdb/. Crystal structures of nucleic acids should
continue to be submitted directly to the Nucleic Acid Database.
After data has been deposited, it will be processed immediately by the RCSB
and returned to the author. For most cases, files will be released within
one week of their arrival at PDB or immediately following their release
from a HOLD status. This time is based upon the extensive testing done by
the RCSB over the past three months.
The files released by the RCSB will be in a fully processed and final
format.
Structures deposited prior to January 27, 1999 will be processed and
released according to the Layered Release Protocol previously described in
the PDB Newsletter of October 1997, January 1998, and April 1998. BNL will
be responsible for the completion of the processing of all files received
up to that point.
In the near future, the RCSB will introduce a new Web-based tool for
deposition called the AutoDep Input Tool (ADIT) at the RCSB Web site. The
features of ADIT are described below. During the transition period, both
AutoDep and ADIT will be available to depositors.
Questions about deposition should be sent to deposit@rcsb.rutgers.edu.
STATUS OF QUERY DURING TRANSITION PERIOD
During the transition period, which ends in October 1999, the two query
engines currently available from BNL (PDBLite and 3DB Browser) will
continue to be maintained by BNL and made available the BNL PDB Web sites.
Additionally, new query engines will be introduced at the RCSB Web sites.
Anyone using the PDBLite or 3DB Browser query engines at the BNL Web site
or any of its mirrors should be able to continue to use those services.
New query engines have been developed by the RCSB, and these will be
introduced during the transition year. The aim of these query engines is to
provide basic and more complex query capabilities for the PDB in convenient
forms. The basic level query engine is called SearchLite. This
keyword-based query system is the subject of an article in this newsletter.
(See "New PDB Web Tools.") Although the scope of the SearchLite query
engine is to provide basic query capability, this engine nevertheless
exposes the information content and accompanying services provided by the
RCSB PDB. The SearchLite query engine is available from the RCSB PDB Web
site, and we encourage users to try it out.
A prototype version of a query engine that supports more advanced queries
has been developed, and alpha testing is beginning. This engine will be
made available in two phases later this year after a thorough testing and
evaluation process.
STATUS OF DISTRIBUTION DURING TRANSITION PERIOD
During the transition period, the PDB will be accessible from two Web
sites: one reflecting the RCSB PDB and one reflecting the BNL PDB. Both
sites will maintain the current version of the PDB FTP archive. The FTP
archive will remain in its current form.
The RCSB PDB Web site provides the PDB FTP archive, up-to-date transition
information, and access to new features of the RCSB PDB system as they
become available. These new features, described below, will include more
complex query searching, a new data deposition tool, and a structure
validation server. The BNL PDB Web site will provide the PDB FTP archive,
AutoDep, PDB Lite, and 3DB Browser and its related resources.
Structures will be released weekly by the RCSB to all PDB Web sites.
In the future, additional RCSB mirrors will be made available.
-----------------------------------------
mmCIF AND PDB FORMATS IN THE RCSB PDB
The RCSB will continue to accept and distribute coordinates in the mmCIF
and PDB formats. The PDB format released by the RCSB will be uniform and
will continue to use the four-character PDB identifier.
Internally, the RCSB uses the macromolecular Crystallographic Information
File (mmCIF) [1] format to process data. mmCIF is the IUCr-approved data
representation for macromolecular structures. The mmCIF dictionary, a
collection of more than 1,600 definitions, provides the basis for the
RCSB's integrated data processing and query system.
Structures can be deposited in PDB format and then are converted to an
mmCIF format file using software developed by the RCSB.
mmCIF information and resources are available at
http://ndbserver.rutgers.edu/mmcif/.
1. P.E. Bourne, H.M. Berman, B. McMahon, K.D. Watenpaugh, J. Westbrook, and
P.M.D. Fitzgerald. The Macromolecular Crystallographic Information File
(mmCIF). Meth. Enzymol. (1997) 277, 571-590.
-----------------------------------------
RCSB PDB MEETINGS AND PRESENTATIONS
Presentations Planned for 1999
Presentations September 1998 - January 1999
Discussion of the RCSB PDB, December 13, 1998, in Asilomar, CA
PLANNED RCSB PRESENTATIONS 1999
Meeting/Seminar Date/Location/Attendee
Finding the Path: Issues of Access January 27-28, 1999
to Research Resources Washington, DC
National Science and Technology Helen M. Berman
Council Committee on Science,
Subcommittee on Biotechnology.
Argonne National Laboratory February 11, 1999
Chicago, IL
Helen M. Berman
NIGMS Structural Genomics Targets February 11-12, 1999
Workshop Washington, DC
Helen M. Berman
Biophysical Society Annual Meeting February 13-17, 1999
Baltimore, MD
Helen M. Berman
The Association of Biomolecular Resource March 19-22, 1999
Facilities '99: Bioinformatics and Durham, NC
Biomolecular Technologies Helen M. Berman, Phil Bourne
The Sealy Center Fourth Symposium on March 19-21, 1999
Structural Biology Galveston, TX
Helen M. Berman
Data Mining Course May 12-23, 1999
Erice, Italy
Helen M. Berman, Phil Bourne
American Crystallographic Association May 22-27, 1999
Annual Meeting Buffalo, NY
Helen M. Berman, Phil Bourne,
Gary Gilliland, John Westbrook
Eleventh Conversation in Biomolecular June 15-16
Stereodynamics Albany, NY
Helen M. Berman
International Union of Crystallography August 4-13, 1999
Congress and General Assembly Glasgow, Scotland
Helen M. Berman, Phil Bourne,
John Westbrook
RCSB PRESENTATIONS (SEPTEMBER 1, 1998-JANUARY 22, 1998)
Meeting/Seminar Date/Location/Attendee
CCP4 Data Harvesting Meeting September 16-19, 1998
Cambridge, United Kingdom
Helen M. Berman
Structure-based Functional Genomics October 4 -7, 1998
Avalon, NJ
Helen M. Berman, John Westbrook,
Phil Bourne, Gary Gilliland
1998 Cold Spring Harbor Laboratory October 14-27, 1998
(CSHL) Macromolecular Crystallography Cold Spring Harbor, NY
Gary Gilliland, Phil Bourne,
Helen M. Berman
United States National Committee for November 8, 1998
Crystallography Meeting Washington, DC
Helen M. Berman
SC98: High Performance Networking November 7-13, 1998
and Computing Conference Orlando, FL
Phil Bourne
Molecular Modeling in the Large December 6-10, 1998
San Diego, CA
Phil Bourne
RNA Informatics Workshop December 8-11, 1998
Arlington, VA
Helen M. Berman
Bristol-Myers Squibb December 17, 1998
Princeton, NJ
Helen M. Berman
DOE Computational Structural Biology December 18-19, 1998
Research Meeting Monterey, CA
Gary Gilliland
Pacific Symposium on Biocomputing '99 January 4-9, 1999
Big Island, HI
Phil Bourne
Keystone Symposium: Frontiers of NMR January 9-15,1999
in Molecular Biology VI Breckenridge, CO
Gary Gilliland, Diane Hancock
International Symposium on Structural January 11-12, 1999
Biology and Genomics Tsukuba, Japan
Helen M. Berman
DOE Contractor and Grantee Genome January 12-16, 1999
Progress Workshop Oakland, CA
Gary Gilliland
RCSB WORKSHOPS
Meeting Date/Location/Attendee
Data Processing and Annotation October 15-16, 1998
Workshop Piscataway, NJ
Helen M. Berman, Gary Gilliland,
John Westbrook
Meetings with protein modeling groups December 8-9, 1998
Piscataway, NJ
Helen M. Berman, John Westbrook,
Phil Bourne
December 11, 1998
San Diego, CA
John Westbrook, Phil Bourne
December 12-13, 1998
Asilomar, CA
Helen M. Berman, Phil Bourne,
John Westbrook
OPEN DISCUSSION OF THE RCSB PDB AND ITS ROLE IN MODELING AND
STRUCTURE PREDICTION DECEMBER 13, 1998, ASILOMAR, CA
Leveraging the CASP3 meeting in Asilomar, California, the RCSB held a
workshop on December 13, 1998. The aim of this workshop was to report on
the status and plans for the PDB and to engage a large subset of users of
the PDB in open discussions on future direction and policy. The meeting was
chaired by Helen Berman and Phil Bourne and was attended by key
representatives from Glaxo Wellcome, MRC, Columbia University, NIH,
University College London, University of Wisconsin, Rutgers University, UC
San Diego, EBI, Molecular Simulations, Inc. and Stanford University. The
meeting began with introductions of all participants and a statement of
purpose to provide information, address concerns, and gain input.
Helen Berman described the two grand challenges for the RCSB as the goals
of (1) relating sequence, structure, and function and (2) helping
researchers, educators, and industry. These challenges need to be met in
the face of an increase in both the number and variety of users.
Helen then provided an overview of all aspects of RCSB PDB. The key
features of the RCSB resource were described as rapid and reliable data
processing, a commitment to uniform data, versatile query and reporting
capability for individual structures across the archive, and links to other
data.
RCSB data processing is a single integrated system for deposition,
annotation, validation, database management, and archiving. The system is
based on a community reviewed standard (CIF) and should scale automatically
with new content and technology. The data-processing system is adaptable
for different types of molecule (protein, nucleic acid), handles multiple
input and output formats, can be used for primary deposition and for
creating data uniformity, and can be customized according to the type of
experiment (e.g., X-ray, NMR). The deposition system is designed to accept
Web input and rapidly return annotated and validated entries. Information
provided to the depositor includes information on sequence neighbors,
structural neighbors, experimental validation, and a validation summary
(ProCheck, Nucheck, SFCheck). In the future, it is expected that the
deposition component will be distributed, the ligand database will be
integrated, data harvesting approaches will be integrated, and more links
to other resources will be added.
In discussion, it was pointed out that there is a strong synergy between
data quality and obtaining reliable results from queries. A great deal of
difficulty in obtaining reliable information from searches across the
database can be avoided if the structure files were processed in a
consistent manner. Query features supported by the new search engines
include iterative queries, multiple structure analysis, and resources
including structure alignments and neighboring.
Electronic distribution of the PDB will continue with SDSC as the primary
distribution site and a network of mirrors and partial mirrors. A CD-ROM of
the PDB will be distributed from NIST which will maintain the master
archive. Outreach efforts will continue and involve the community of
depositors, users, and software developers via the help desk, newsletter,
and Web.
John Westbrook described data-processing requirements and the system being
established at the RCSB. Requirements of the data-processing system include
the ability to capture information in a flexible and efficient manner,
store information in a well defined and uniform manner (facilitating query
and exchange), and use methods of information technology that will scale
well with volume and content. The data representation is the mmCIF
standard, for which the dictionary has currently more than 1,700
definitions. This representation defines relationships between data items,
types, range restrictions, and allowed values. The representation uses a
simple table-like organization of data and data definitions. Furthermore,
the dictionary is fully software-accessible. This standard representation
received a detailed community expert review, is maintained by the IUCr,
evolves with science, and is a foundation for data exchange and
interoperability. A point that was stressed is that dictionaries
are key to data processing: they provide a standard electronic description
of all terminology, they make software extensible to changes and content in
data, and they provide a framework in which to handle reference data (e.g.,
ligands, modified amino acids).
Phil Bourne provided an overview of the PDB query systems that are being
implemented. They include systems that support basic and complex queries.
Helge Weissig gave a computer demonstration of the SearchLite system that
will be available in the first phase of the RCSB implementation.
-----------------------------------------
NEW PDB WEB TOOLS
1.SearchLite
2.ADIT
3.Validation Server
SEARCHLITE: VERSION 1.0 OF THE PDB WEB INTERFACE
The RCSB has developed a set of query and structure reporting tools for use
with the PDB. These tools will continue to evolve with each release of the
RCSB PDB Web site. Two sets of upwardly compatible enhancements to the
query capability are planned for release later in 1999.
A user accesses the PDB through the Web by making a query and receiving a
result. These actions are shown on the left- and right-hand side of Figure
1, respectively. Each of these two components will evolve with every new
release of the Web interface. Two further upwardly compatible enhancements
are planned for 1999. This article discusses only version 1.0, which is
available now. Future newsletters will discuss new versions as they become
available. To simplify the discussion, the query and subsequent result are
discussed separately.
[Figure 1. PDB Query and Result Overview]
-- Query
Version 1.0 of the query interface is a keyword query: a user supplies one
or more keywords, and all structures that contain those keywords are
returned. The search for keywords is performed on the contents of the PDB
files. To make a more specific query, a user may pose the query to a subset
of PDB record types. For example, a search for Jones will find many
structures for which Jones is not an author but which, for example, were
solved using the map-fitting programs developed by Alwyn Jones. Restricting
the search field to just author returns structures for which Jones was an
author according to PDB JRNL and REMARK 1 records.
Multiple keywords can be used as part of the same query. A query term of
protein kinase will return all references to structures that contain
references to the terms "protein" and "kinase." Since "protein" is a
general term and appears in nearly all structures, this becomes a search
for "kinase" and will return, for example, "histidine kinase," which is not
a member of the protein kinase family. Using the search term "protein
kinase" (in quotes) requires the keywords to be contiguous, which will
return a set of structures closer to those belonging to the protein kinase
family. However, it will also return structures that contain the phrase
"protein kinase inhibitor," which may not be desired. There is no NOT
clause supplied at present to refine this query to exclude the keyword
"inhibitor." Results from such queries can be manually trimmed or added to
as desired.
-- Results
Fig. 1 shows two types of results presented for a given query -- a single
structure result or a multiple structure result. For example, entering a
specific PDB identifier will return a single structure, whereas a phrase
such as "protein kinase" will return multiple structures. Each case is
discussed separately.
Single Structure
A single structure result will return an Explore page. As the name
suggests, the page provides the opportunity to further explore several
different aspects of the structure, both from the PDB and elsewhere on the
Internet. The Explore page presents summary information about the
structure, including the release date, author names, compound name, and
primary citation, and a dynamic list of options based upon what information
is available for the specific structure. For example, if the structure is a
crystal structure of a nucleic acid or nucleic acid complex, a link will
appear to the Nucleic Acid Database Atlas page (NDB; Berman et al. (1992)
Biophys J. 63(3), 751-9). The NDB Atlas Entry provides further summary
information, hand-curated images, and highly curated coordinate files.
Similarly, if a previous version or versions of a structure exist, the page
links to a review of the chronology of that particular structure. If no
previous versions exist, the link will not appear. Other options that
appear on the Explore page are described below.
View Structure -- Provides still and interactive views of the structure.
Still images at different sizes and resolution are produced on the fly with
Molscript (Kraulis (1991) J. App. Cryst. 24, 946-950) and Raster-3D
(Merritt and Bacon (1997) Methods in Enzymology 277, 505-524). Images are
displayed in a standard orientation (right-hand frame x-axis horizontal,
y-axis vertical, looking down the z-axis) and use the author-deposited
secondary structure assignments to denote secondary structure as ribbons or
cylinders. Interactive views use a standard VRML browser and the Molscript
VRML output option (Kraulis loc. cit.), Rasmol (R. Sayle and E.
Milner-White (1995) TIBS 20(9), 374), or the QuickPDB Java applet
(Shindyalov and Bourne, unpublished).
Download Coordinates -- Lets users download atomic coordinates in PDB or
mmCIF format either as uncompressed ASCII files or compressed with UNIX
compress, gzip, or pkzip.
Structure Neighbors -- Provides direct access to reports of other
structures exhibiting 3-D structure homology to the structure being
explored. Access is provided to the databases of the common classification
methods: CATH (Orengo, Michie, Jones, Jones, Swindells, and Thornton (1997)
Structure 5(8), 1093-1108); CE (Shindyalov and Bourne (1998) Protein
Engineering 11(9), 739-747); FSSP (Holm and Sander (1998) Nucl. Acids Res.
26, 316-319); SCOP (Murzin, Brenner, Hubbard, and Chothia (1995) J. Mol.
Biol. 247, 536-540) and VAST (Gibrat, Madej and Bryant (1996) Current
Opinion in Structural Biology 6, 377-385).
Geometry -- Provides a tabular and graphical (requires Rasmol)
representation of the stereochemistry of the structure. Both are
color-coded to indicate deviation from the standard values reported by Engh
and Huber (1991) Acta Cryst. A47, 392-400. Sequence Information -- Reports
the size and molecular weight of each chain in the macromolecule as well as
the sequence, and in the case of protein chains, the secondary structure
assignment according to Kabsch and Sander ((1983) Biopolymers 22(12),
2577-2607).
Previous Versions -- Provides a graphical summary of the release and
withdrawal dates of previous versions of a structure and a tabular
comparison of the different features within each version. Stereochemical
comparisons between each version of the structure are also presented.
Crystallization Information -- Reports data where available from the
Biological Macromolecular Crystallization Database (BMCD; Gilliland et al.
(1994) Acta Cryst. D50 408-413). These data includes details of the
crystal(s), crystallization conditions, and references.
Other Sources -- Provides pointers to other relevant information available
via the Web. Again, this is a dynamic list. What appears depends on the
structure in question.
Multiple Structures
Queries that return multiple structures are subject to three actions:
filtering, downloading, and summarizing. Each is discussed separately.
Filtering -- A single structure, a subset of structures, or all structures
can be chosen for downloading or summarizing. Alternatively, the selected
list of structures can be used as input to a subsequent query, refining the
search.
Downloading -- The selected list of structures can be downloaded as a set
of PDB files or mmCIFs in compressed or uncompressed formats. Sequences
only, taken from the PDB SEQRES records, can be downloaded in FASTA format.
Summarizing -- Reports on the selected list of structures can be generated.
They can be presented as formatted Web pages (HTML) for printing or as
tables with delimited fields suitable for loading into a spreadsheet or
user-provided program (TEXT). Reports are available for cell constants and
space group, primary citation, sequence, experimental technique, and
refinement details (where applicable).
-- Summary
The basic structure for making a query and interpreting results described
here will form the basis of more powerful query capabilities in the future.
Examples of such queries will be reported in future issues.
-- Acknowledgements
The RCSB is grateful to Drs. Steven Brenner and Paula Fitzgerald for beta
testing v1.0 of SearchLite.
ADIT: AUTODEP INPUT TOOL
A new deposition software tool, called the AutoDep Input Tool (ADIT), has
been developed by the RCSB. This tool will be made available at the RCSB
Web site for testing during the initial part of the transition period and
subsequently made available as an alternative to the existing AutoDep
system.
ADIT is a Web-based deposition tool that builds a collection of HTML forms.
Each form presents data items selected from a single mmCIF category. The
scope of all possible data items available to ADIT is determined by the
content of an underlying mmCIF data dictionary. Because this dictionary
contains more than 1,600 definitions, the most important function of the
view is to present to the ADIT user those data items that are relevant to
deposition.
ADIT is undergoing beta testing by members of the crystallographic and NMR
spectrographic communities. The test period will extend until the system
has been found to be robust by depositors and the archive. We expect this
test period to last two to four months. Following testing, ADIT will be
made available for general use. ADIT, used with a specialized view for
annotation, is used by the RCSB to process structures deposited to the PDB.
ADIT: VALIDATION SERVER
The RCSB has released its validation server
(http://pdb.rutgers.edu/validate/) at the RCSB Web site. This validation
server can be used to check the format consistency of the coordinates and
perform a validation pre-check of the structural features and structure
factors before the structure is deposited. The validation server will
accept coordinate and structure factor data and produces a report of
geometrical and experimental checks. The content and presentation of
the validation report is the same as the report produced during the
deposition process and can be used by the depositor prior to deposition or
at any time during a structure refinement.
Tutorials are available online.
-----------------------------------------
PDB E-MAIL DISCUSSION GROUP
As of February 3, 1998, the PDB e-mail discussion group (the PDB
listserver) will be maintained by the RCSB PDB staff. The purpose of this
discussion group is to facilitate open discussion of topics related to
macromolecular structure. These topics are not necessarily limited to the
PDB. For example, problems in structure analysis, job ads, and requests for
information relating to protein structure are legitimate postings. Personal
messages, abuse, and messages of unrelated commercial nature are not
acceptable.
At this time, all messages should be posted to the RCSB listserver and
postings to the BNL listserver should cease -- i.e. people should
discontinue using the BNL PDB list and listserver addresses. To ensure
uninterrupted service, a grace period of two months is being provided in
which any messages that are inadvertantly posted to the BNL PDB listserver
will be transfered to the RCSB PDB listserver. The complete mailing list
archive will be maintained by the RCSB at
http://www.rcsb.org/pdb/lists/pdb-l archive.
Current subscribers to the BNL PDB listserver will be automatically
transferred to the RCSB PDB listserver, and instructions on posting to the
new listserver will be provided by e-mail. New users may subscribe by
sending the command
subscribe pdb-l
in the body of an e-mail message to majordomo@rcsb.org. Instructions on
mailing to the list will then be returned by e-mail. Any user who wishes to
be removed from the listserver should send the message
unsubscribe pdb-l
to majordomo@rcsb.org.
The current RCSB operating policy for the discussion group is that it will
not be moderated but only subscribers can to post to it. The purpose of
this policy is to permit uncensored access to the group while avoiding
external junk mail. Our mechanism for checking that a sender is subscribed
is to check the complete e-mail address against the subscription list. This
mechanism means that senders must be sure that the address from which they
are posting is the same as the one from which they subscribed. In cases
where persistant delivery problems are detected, the RCSB reserves the
right to remove addresses from the list.
-----------------------------------------
LINKING TO THE PDB THROUGH YOUR BROWSER
Articles in this newsletter have described the search query capabilities at
the RCSB PDB site and have given a glimpse of extended capabilities that
will become available in the future. However, a PDB user with a Web
resource may wish to build structure retrieval mechanisms into the resource
Web pages. To facilitate this type of activity, the CGI scripts at the RCSB
PDB Web site may be used directly from a user's own Web page. For single
structure retrieval, it is only necessary to provide an URL of the form
http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=XXXX
with the (case-insensitive) XXXX replaced by the four letter identification
code for the respective entry. The URL will return to the browser the
"Structure Explorer" page corresponding to that entry and this page allows
a direct download of the corresponding cooordinate file. For example, the
URL http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2cpk will return the page
on structure entry 2cpk.
An illustrative html code fragment that shows how to incorporate a CGI
script at the RCSB PDB site for returning multiple entries to the browser
is
in which the series of XXXX's may be replaced on the Web page by the
four-letter identification codes for the required entries. This code
fragment will create an "Import to PDB" button with an associated parameter
field in which you may enter the PDB entry codes.
As a concrete example, the code fragment