------------------------------------------------------------------------
PROTEIN DATA BANK
Quarterly Newsletter
Release #74 - October 1995
------------------------------------------------------------------------
INTERNET SITES
WWW.....................http://www.pdb.bnl.gov
FTP (anonymous).........ftp.pdb.bnl.gov
Gopher..................gopher.pdb.bnl.gov
------------------------------------------------------------------------
OCTOBER 1995 PDB RELEASE
3821 full-release atomic coordinate entries
Molecule Type
-------------
3469 proteins, peptides, and viruses
80 protein/nucleic acid complexes
260 nucleic acids
12 carbohydrates
Experimental Technique
----------------------
120 theoretical modeling
490 NMR
3211 diffraction and other
Total size of atomic coordinate entry database is 1350 Mbytes uncompressed.
------------------------------------------------------------------------
TABLE OF CONTENTS
What's New at the PDB
Managing the Archives
Proposed Changes
HET Groups
CIF from PDB Entries
PDB Format Change Policy
To be Ala or Not to be Ala? That is the Question
PDB Structure Factor Files in CIF - A Proposal
Examples of SF Files in CIF
DALI - Server for Protein Structure Database Searches in 3D
WHATCHECK - Tool for Verification of Protein Structures
Biotech Protein Structure Validation Server Now On-Line
Notes of a Protein Crystallographer
Professor M. G. Replacement's 65th Birthday
CIF Workshop at 1995 Annual ACA Meeting
Order Form
Affiliated Centers
------------------------------------------------------------------------
WHAT'S NEW AT THE PDB
In order to make it easier to exchange the structure factors, i.e.,
the observed experimental data from X-ray crystallographic experiments,
the PDB, in close collaboration with a number of macromolecular
crystallographers, has developed a proposed standard interchange
format for structure factors. This standard is in CIF, which stands
for the IUCr-developed `Crystallographic Information File'. It was
chosen both for simplicity of design and for being clearly
self-defining, i.e., that the top of the file contains sufficient
information for the rest of the file to be read and understood by
either a program or a person. It thus allows for an archival record
of the data to be stored for future use. This format will be easy
to extend, just by adding additional tokens to the top of the file,
as new crystallographic experimental methods are developed.
This project has been lead by Dr. Vivian Stojanoff of the BNL Biology
Department, who has worked closely with the Chairperson of IUCr Working
Group on Macromolecular CIF, Dr. Paula Fitzgerald, and other members
of this committee. Vivian recently presented this standard at the CIF
Workshop held during the Annual ACA Meeting in Montreal, Canada (see
relevant articles in this Newsletter - one summarizing the Workshop and
another presenting details of the format). We encourage all depositors
of X-ray structures to submit their structure factors and to do so in
this format. In fact, over the years, the PDB has observed that one of
the most useful reasons for storing structure factors is for the
crystallographer who did the experiment to be able to retrieve his/her
own data which may be misplaced in their laboratory. In parallel, it
will likely foster a great deal of research into methods of structure
determination and validation techniques based on comparison of the
final models versus the experimental data. All of the presently
deposited structure factors have been converted to this format and
are available via WWW. In addition, the PDB is providing simple filters
which convert between this sfCIF format and other prominent formats,
such as those in PROLSQ, TNT, X-PLOR and the CCP4 package.
Joel L. Sussman
------------------------------------------------------------------------
MANAGING THE ARCHIVES
This article inaugurates a regular column that will discuss the
contents and format of PDB coordinate entries. We plan to use this
column to alert users of possible changes in our data representation
procedures. We will summarize implementation schedules, major policy
decisions, and related items. For example, we regularly receive
comments and suggestions for improving both the stored data and
access to it. Some of these suggestions have been incorporated into
PDB entries, while others are still being evaluated. In the future PDB
will also provide data in CIF format using the mmCIF data dictionary.
These and other changes in PDB operations require that we keep our
users abreast of the issues - this column is intended to do just that.
The PDB is pleased to announce the appointment of Nancy Oeder Manning
as Outreach Program Coordinator. Included in her responsibilities is
the task of making sure that questions regarding entry content and
format are resolved. If you would like to discuss the issues, please
send e-mail to Nancy at oeder@bnl.gov and/or Enrique Abola at
abola1@bnl.gov. You may also send a message to a larger audience via
our listserver (pdb-l@pdb.pdb.bnl.gov).
We suggest keeping a close watch on the PDB Format Description
document available through our Internet sites (WWW, FTP, and Gopher).
This document will reflect changes in PDB Format and will serve as
the reference for all questions regarding the content and format of
PDB entries.
A common concern is the time frame for incorporating announced changes
into existing entries. There are several reasons for the delay in
implementation of changes. The first of these was the need to formulate
a clear policy on how changes to the entry content and data format are
to be introduced and implemented. We have developed the protocol
detailed in the following article. The policy will become effective
after a short period of public discussion.
Proposed Changes
Professor George Sheldrick, University of Göttingen, Germany, suggested
that we use B-equivalent in ATOM/HETATM records instead of U-equivalent
when anisotropic temperature factors are included in an entry. This
will obviate the need to check if ANISOU records are present before
interpreting the contents of the B-value field. A number of entries
recently deposited have anisotropic thermal parameters. Some of these
resulted from studies by Keith Wilson and collaborators on very high
resolution structures. George Sheldrick also deposited a structure,
refined by SHELX, that includes anisotropic thermal parameters and he
requested that the B-value field contain B-equivalent instead of
U-equivalent.
We acknowledge the merit in this suggestion and do not foresee any
major impediments to its adoption. Since there are only a few entries
containing ANISOU values that will be affected by this change, at the
request of Professor Sheldrick, his entry will be released with the
B-equivalent values.
HET Groups
The number of heterogen groups stored in the PDB is rapidly growing.
Users have been requesting improvements in representation and handling
of these groups. There are a number of initiatives underway in response
to these requests and suggestions. Most important is the collaboration
recently initiated with the Cambridge Crystallographic Data Centre
(CCDC). As part of this work CCDC has provided the PDB with PreQuest,
the processing program they use in preparing new entries for inclusion
into their database. This program will help PDB in representing and
managing this growing data set.
This software allows us to build 2-D diagrams of the HET groups from
the 3-D coordinates. It automatically generates an atom numbering
scheme using a standard algorithm. Matching of the 2-D atom names
to those used in the crystal study is also provided. It then becomes
less important to follow conventions such as IUPAC when naming atoms.
IUPAC conventions for atom nomenclature are difficult to use in
computer-based applications. Attempts have been made to follow
them over the years; however, as users are aware, violations have
occurred because of the difficulties involved in representing
heterogens.
The PDB will keep users abreast of major developments in this area.
Our WWW server (http://www.pdb.bnl.gov) contains a link to our
heterogen collection and also to other databases that provide
additional information about these groups.
CIF from PDB Entries
The latest macromolecular CIF (mmCIF) dictionary containing definitions
for items normally found in PDB entries has recently been released by
the working group commissioned by the IUCr. This dictionary uses the
CIF standard and is available through PDB's Internet sites (WWW, FTP,
and Gopher) for study and comment. PDB is mounting a major effort to
read and write CIF coordinate entry files. Frances Bernstein is
currently building a table to relate PDB fields to CIF tokens. Once
this table is ready it will be shared with the community along with
tools that have been developed for handling PDB entries in CIF.
Comments on this column should be sent to Enrique Abola
(abola1@bnl.gov) or Nancy Oeder Manning (oeder@bnl.gov).
------------------------------------------------------------------------
PDB FORMAT CHANGE POLICY
The PDB will use the following protocol in making changes to the way
PDB coordinate entries are represented and archived. The purpose of
the new policy is to allow ample time for everyone to understand these
changes and to assess their impact on existing programs. These
modifications are necessary to address the changing needs of our
users as well as the changing nature of the data that is archived.
1. Comments and suggestions will be solicited from the community
on specific problems and data representation issues as they
arise.
2. Proposed format changes will be disseminated through the PDB
Listserver (pdb-l@pdb.pdb.bnl.gov) and PDB's Internet sites
(WWW, FTP, and Gopher). They will also be summarized in the
PDB Quarterly Newsletter.
3. A sixty-day discussion period will follow the announcement of
proposed changes. Comments and suggestions must be received
within this time period. Major changes which are not upwardly
compatible will be allotted up to twice the standard amount of
discussion time.
4. This sixty-day discussion period will be followed by a
thirty-day period in which the PDB staff, the PDB Advisory
Board, and the User Group Chair will evaluate and reconcile all
suggestions. The final decision pertaining to the format change,
which lies with the Advisory Board Chair, will then be officially
announced via the PDB Listserver and PDB's Internet sites (WWW,
FTP, and Gopher).
5. Implementation will follow official announcement of the format
change. Major changes will not appear in PDB files earlier than
sixty days after the announcement, allowing sufficient time to
modify files and programs.
6. Changes will be released no more than twice a year, unless
extraordinary circumstances require action. This will be done
only in consultation with the Advisory Board and following the
usual ninety-day discussion and evaluation period.
The PDB format has been in use since the late 1970's. A number of
groups including the mmCIF Committee have been looking at ways to
upgrade both the file content and the interchange format used by PDB.
This is clearly needed due to changes in the data that PDB archives,
the size of the database itself, and finally, to allow us to use more
up-to-date methods for representing and storing biological data.
The PDB plans to be prudent and deliberate in making changes to the
current PDB files in order to minimize the need to change existing
programs. In particular, we will explore ways and means of ensuring
that programs which read the current ATOM/HETATM records can continue
to do so in the foreseeable future.
Finally, we wish to acknowledge Dr. Gerald Selzer of the National
Science Foundation who urged us to formulate this policy.
Any questions, comments, or suggestions should be sent to
Joel Sussman (jls@bnl.gov), Enrique Abola (abola1@bnl.gov), or
Dave Stampf (drs@bnl.gov).
------------------------------------------------------------------------
TO BE ALA OR NOT TO BE ALA? THAT IS THE QUESTION.
The SEQRES records in each PDB entry represent the complete sequence
of the molecule studied. The sequence that appears on ATOM records
must match the SEQRES records. It is essential that each depositor
answer the sequence-related questions in the PDB Electronic Deposition
Form.
One issue that continues to cause problems is addressed in the
Deposition Form but often not handled correctly in the coordinate
files that are actually sent to the PDB. Following is text taken from
the Deposition Form:
Some procedures force users to identify residues as
ALA when side-chain atoms are missing from the density.
However, the correct residue name must be used in your
deposition, both in the coordinate and SEQRES records.
It is important to recognize the difference between a residue that
is identified as ALA because it actually is alanine and a residue for
which the side chain atoms could not be located in the electron
density maps. In the latter case the residue must be given the
correct residue name. When these instructions are not followed, we
have a great deal of difficulty in determining whether a residue that
does not match the sequence database is a mutation that we were not
told about, if it is a misnamed ALA (for example), or if there is
some other reason for the mismatch.
In a similar vein, there is a distinction that must be made between
the following possible situations:
1. The atoms of residues 45 - 50 could not be located in the
experiment. In this case residues 45 - 50 will be included
in the SEQRES records although no coordinates are present
in the PDB entry.
2. A recombinant experiment was done so residues 45 - 50 are not
present in the protein and residue 51 forms a normal peptide
bond with residue 44. In this case the SEQRES records will not
include residues 45 - 50 because they were not present.
3. Residues 45 - 50 are excised from the protein and there are
now two chains instead of one. In this case the protein will
be presented as two separate chains and residues 45 - 50 will
not appear in the PDB entry.
Providing the necessary information on the Deposition Form will allow
us to prepare entries for your structure more quickly and, most
importantly, correctly.
------------------------------------------------------------------------
PDB STRUCTURE FACTOR FILES IN CIF A PROPOSAL
A standard ASCII interchange format for structure factor files based
on the CIF format has been developed by the PDB in collaboration with
several macromolecular crystallographers. The work was presented by
its primary developer, Dr. Vivian Stojanoff of the BNL Biology
Department at the CIF Workshop held during the ACA Annual Meeting in
Montreal, Canada. The importance of a standard for the submission and
retrieval of structure factor data as well as its role in structure
validation procedures was discussed.
Structure factor files are received by the PDB for archiving and
redistribution in a variety of formats. These files have to be
converted by users to the different data input formats required by
analysis programs. The purpose of the new standard is to provide a
unique submission and retrieval format for structure factors from the
PDB. In addition, it will facilitate the interchange of data between
laboratories. The proposed standard is in CIF and was prepared in
consultation with Dr. Paula Fitzgerald, Chairperson of the IUCr
Working Group on Macromolecular CIF. A number of the data names
presented should be considered provisional, as they have not yet
been formally approved by the IUCr. However, no substantial changes
are anticipated in this part of the mmCIF dictionary.
The proposed standard is compatible with most crystallographic
packages, such as CCP4, PROLSQ, TNT, X-PLOR, SHELXL93, SFTools,
etc. A parser (filter) which converts this format into other
standard formats will be distributed by the PDB. The examples
presented below illustrate the proposed format. Included in the
standard are provisions to accommodate a variety of data items
from experiments such as multiple wavelength anomalous scattering.
A full description and other examples may be accessed through PDB's
Internet sites (WWW, FTP, and Gopher).
Comments and suggestions are welcome; please send them to Enrique Abola
(abola1@bnl.gov).
Examples of SF Files in CIF
- First Example
This example is one of the simpler possible cases, in which the
depositor has provided measured and calculated structure factors
and calculated phases.
Those reflections that have _refln.status set to 'o' were considered
observed and were used in refinement. The reflection with _refln.status
set to 'f' indicates that the reflection was considered observed but
has been excluded from refinement for the purposes of calculating an
R-free value.
data_r1aaksf
loop_
_database_2.database_code
_database_2.database_id
pdb_sf 'R1AAKSF'
pdb_coords '1AAK'
_audit.creation_date '1992-04-08'
loop_
_audit_author.name
'COOK,W.J.'
'JEFFREY,L.C.'
'SULLIVAN,M.L.'
'VIERSTRA,R.D.'
#COMPND UBIQUITIN CONJUGATING ENZYME (E.C.6.3.2.19)
#SOURCE (ARABIDOPSIS THALIANA)
#AUTHOR W.J.COOK,L.C.JEFFREY,M.L.SULLIVAN,R.D.VIERSTRA
#REMARK 2
#REMARK 2 RESOLUTION. 2.4 ANGSTROMS.
#REMARK 3
#REMARK 3 REFINEMENT.
#REMARK 3 PROGRAM 1 X-PLOR
#REMARK 3 AUTHORS 1 BRUNGER
#REMARK 3 PROGRAM 2 PROLSQ
#REMARK 3 AUTHORS 2 KONNERT,HENDRICKSON
#REMARK 3 R VALUE 0.22
#REMARK 3 RMSD BOND DISTANCES 0.025 ANGSTROMS
#REMARK 3 RMSD BOND ANGLES 2.8 DEGREES
#CRYST1 41.800 44.900 83.200 90.00 90.00 90.00 P 21 21 21 4
loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.F_meas_au
_refln.F_calc_au
_refln.phase_calc
_refln.status
0 0 18 553.600 538.455 180.00 o
0 0 20 783.700 781.204 80.00 o
.
.
.
17 3 4 21.100 145.713 23.03 o
17 3 63.800 81.747 291.83 f
17 4 0 52.000 40.654 270.02 o
- Second Example
In this example, the depositor has provided measured and calculated
structure factors, calculated phases, measured sigmas, and three
sets of heavy-atom derivative data.
data_r1bsrsf
loop_
_database_2.database_code
_database_2.database_id
pdb_sf 'R1BSRSF'
pdb_coords '1BSR'
_audit.creation_date '1993-04-28'
loop_
_audit_author.name
'MAZZARELLA,L.'
#COMPND RIBONUCLEASE (BOVINE, SEMINAL) (BS-RNASE)
#SOURCE BOVINE (BOS TAURUS) SEMINAL FLUID
#AUTHOR L.MAZZARELLA
#REMARK 2
#REMARK 2 RESOLUTION. 1.9 ANGSTROMS.
#REMARK 3
#REMARK 3 REFINEMENT.
#REMARK 3 PROGRAM X-PLOR
#REMARK 3 AUTHORS BRUNGER
#REMARK 3 R VALUE 0.177
#REMARK 3 RMSD BOND DISTANCES 0.020 ANGSTROMS
#REMARK 3 RMSD BOND ANGLES 3.70 DEGREES
#CRYST1 36.500 66.700 107.500 90.00 90.00 90.00 P 2 21 21 4
loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.F_meas_au
_refln.F_calc_au
_refln.phase_calc
_refln.F_meas_sigma_au
_refln.status
0 0 4 197.8 1351.0 -180.0 1.9 o
0 0 6 733.2 807.0 0.0 7.0 o
.
.
.
19 3 1 157.0 131.2 -145.0 24.2 o
19 3 2 207.6 199.7 -11.8 23.5 o
19 3 4 273.8 374.2 64.1 18.5 o
loop_
_phasing_mir.der_id
_phasing_mir.der_details
HgCl4 'best derivative'
AgNO3_1 'silver nitrate at low concentration - two sites'
AgNO3_2 'silver nitrate at high concentration - six sites'
loop_
_phasing_mir_refln.index_h
_phasing_mir_refln.index_k
_phasing_mir_refln.index_l
_phasing_mir_refln.der_id
_phasing_mir_refln.F_meas_au
_phasing_mir_refln.F_calc_au
_phasing_mir_refln.phase_calc
_phasing_mir_refln.F_meas_sigma_au
0 0 4 HgCl4 197.8 1351.0 -180.0 1.9
0 0 4 AgNO3_1 206.7 1462.0 -180.0 12.3
0 0 4 AgNO3_2 367.3 1551.0 -180.0 36.7
0 0 6 HgCl4 733.2 807.0 0.0 7.0
0 0 6 AgNO3_2 856.6 912.0 0.0 15.4
.
.
.
19 3 1 HgCl4 157.0 131.2 -145.0 24.2
19 3 1 AgNO3_1 142.2 156.3 -112.0 12.7
19 3 1 AgNO3_2 168.3 142.3 -162.0 29.6
19 3 2 AgNO3_1 207.6 199.7 -11.8 23.5
19 3 2 AgNO3_2 183.4 201.9 15.0 25.2
------------------------------------------------------------------------
DALI SERVER FOR PROTEIN STRUCTURE DATABASE SEARCHES IN 3D
This article was written by Chris Sander, European
Molecular Biology Laboratory European Bioinformatics
Institute, Heidelberg, Germany. It describes a service
which may be useful to PDB users.
A database search service allowing exploration of the PDB for structural
similarities is now available on WWW. Developed by Liisa Holm and
Chris Sander of the European Molecular Biology Laboratory European
Bioinformatics Institute (EMBL-EBI) in Heidelberg, with help and input
from Antoine Daruvar and Reinhard Schneider, the server takes protein
structure coordinates and returns a list of all protein structures
judged as similar by the Dali method. Typically, users may want to:
- establish whether a newly determined structure has a unique fold
- find structural homologues not detectable at the sequence level
- explore the spectrum of currently known protein folds
- extract remotely homologous structures for testing of threading
methods
To request a search, go to the PDB WWW site or go directly to
http://www.embl-heidelberg.de/dali/dali.html and follow instructions.
The currently preferred mechanism for submission of search coordinates
is via e-mail to dali@embl-heidelberg.de.
If a user is interested in knowing the structural neighbors of a PDB
protein complete with alignment information or would like to see the
tree organization of all known structures, the Dali search server,
which is linked to the FSSP database [L. Holm and C. Sander, Nucleic
Acids Res. 22, 3600-9 (1994); L. Holm and C. Sander, J. Mol. Biol.
233, 123-38 (1993); L. Holm and C. Sander, TIBS in press (Sept. 1995)],
holds the results of a continuously updated all-against-all
comparison of known protein structures in the PDB. For each
protein in the PDB, its structural neighbors can be retrieved,
complete with alignment information, and, if needed, protein
coordinates optimally superimposed in a common frame of reference.
If a user would like to inspect sequence families grouped around each
protein structure, the Dali server makes use of the continuously
updated HSSP database of PDB/Swissprot alignments [C. Sander and
R. Schneider, Nucleic Acids Res. 22, 3597-9,1994)]. For example,
the Swissprot sequence families (aligned using sequence alignment)
of two remote homologues (aligned in 3D) can be retrieved phased
on the 3D alignment, e.g., the sequence families of actin and hsp70.
For further information, contact Liisa Holm at the EMBL-EBI
(holm@embl-ebi.ac.uk).
------------------------------------------------------------------------
WHATCHECK TOOL FOR VERIFICATION OF PROTEIN STRUCTURES
This article was written by Rob Hooft, European Molecular
Biology Laboratory, Heidelberg, Germany. It describes a
tool which may be useful to PDB users.
A new stand-alone version of the protein structure checking tools
developed as part of the WHAT IF modeling system is now available
for downloading. The stand-alone version, called WHATCHECK, was
developed by Rob Hooft and Gerrit Vriend of the European Molecular
Biology Laboratory (EMBL) in Heidelberg and is being made freely
available to academic and commercial users alike. Crystallographers,
NMR spectroscopists, and modelers interested in using the software
in their own lab should free 80 MBytes of disk space on a Silicon
Graphics machine and download executable and source code via
anonymous FTP from Heidelberg (swift.embl-heidelberg.de/whatcheck),
from the PDB via anonymous FTP (ftp.pdb.bnl.gov/pub/whatcheck), or
from the PDB WWW site (http://www.pdb.bnl.gov). Versions for other
systems may be made available if there is sufficient demand.
The methods in WHATCHECK are based on several years of experience
analyzing protein models and include the following:
- analysis of packing quality
- analysis of backbone conformation and rotamers using a
position-specific residue database
- analysis of the hydrogen bond network, resulting in corrections
to HIS/GLN/ASN side-chain orientations and HISD/HISE/HISH
assignments
- temperature factor analysis
- water molecule position checks
- IUPAC and IUCr convention checks
- a number of geometric checks
WHATCHECK functionality is also part of the Biotech Validation server
available from EBI, PDB, and EMBL.
Questions or suggestions regarding WHATCHECK should be directed via
e-mail to Rob.Hooft@EMBL-Heidelberg.DE.
------------------------------------------------------------------------
BIOTECH PROTEIN STRUCTURE VALIDATION SERVER NOW ON-LINE
This article was written by Chris Sander, European
Molecular Biology Laboratory European Bioinformatics
Institute, Heidelberg, Germany. It describes a service
which may be useful to PDB users.
The Commission of the European Union-funded Biotech partners are:
Shoshana Wodak, Joan Pontius, Alexei Vagin, Jean Richelle
Universitè Libre, Bruxelles, BE
Keith Wilson, Victor Lamzin
EMBL-HH, Hamburg, DE
Chris Sander, Rob Hooft, Gerrit Vriend, Micheal Scharf
EMBL-HD, Heidelberg, DE
Janet Thornton, Roman Laskowski, Malcolm MacArthur
University College London, UK
Rob Kaptein, Ton Rullmann, Jurgen Doreleijers
Bijvoet Center, Universiteit Utrecht, NL
Eleanor Dodson, Gideon Davies, Jan Zelinka, Garib Murshudov
University of York, UK
These partners, in collaboration with the EBI Outstation of the
European Molecular Biology Laboratory (EMBL-EBI) and the Protein
Data Bank, Brookhaven National Laboratory (PDB, BNL), announce a
new WWW service for validating protein structures. The server takes
a set of protein coordinates in PDB format and returns a set of
check reports that evaluate various stereochemical, geometric,
and physical properties. The evaluation is based on careful and
systematic comparison with values derived from a database of
well-determined structures. These checks may be particularly useful
to crystallographers and NMR spectroscopists in the final stages of
structure determination prior to submission of model coordinates to
the public databases. They may also be used to check protein models
built by theoretical methods, such as homology modeling.
The service is now available from three sites:
European Bioinformatics Institute
EMBL-EBI, Hinxton Hall, Cambridge, UK
http://saturn.embl-ebi.ac.uk:8400/
or http://www.embl-ebi.ac.uk/
Protein Data Bank
Brookhaven National Laboratory
Upton, New York, USA
http://biotech.pdb.bnl.gov:8400/
or http://www.pdb.bnl.gov/
European Molecular Biology Laboratory
EMBL-HD, Heidelberg, DE
http://www.embl-heidelberg.de:8400/
or http://www.sander.embl-heidelberg.de/
For further information, contact Chris Sander at the EMBL-EBI
(Chris.Sander@embl-heidelberg.de).
------------------------------------------------------------------------
NOTES OF A PROTEIN CRYSTALLOGRAPHER
Professor M. G. Replacement's 65th Birthday
This article was written by Cele Abad-Zapatero,
Abbott Laboratories, Abbott Park, IL, USA. He
intends to contribute regularly under this heading.
If you have comments or suggestions please contact
him at abad@abbott.com.
Nowadays, it is possible that many older practitioners in the field
of macromolecular crystallography, or even some novices, experience
a sense of deja vu when reading the methodology section of many
crystallographic papers. They have encountered many times sentences
like: `the structure was solved by the method of Molecular Replacement
as implemented in the program suite [...]....'. Or, in a different
context: `the initial phases were improved by non-crystallographic
electron density averaging between the N copies in the asymmetric unit
[...]'. Yet the ideas, concepts, and even the terminology were terra
incognita only thirty years ago. I do not intend to explain the method
here, nor do I intend to statistically show how many macromolecular
structures have been solved by the explicit or implicit use of those
ideas. I just want to pay homage to the person who, approximately
thirty years ago, had the intellectual vision of using the
conservation of protein folds and the `redundancy' of information
in the asymmetric unit to aid in the structure solution of
macromolecular structures.
Professor Molecular G. Replacement was born in Frankfurt, Germany on
July 30, 1930 and emigrated to England with a member of his family
when he was nine years old. He obtained his B.Sc. from the University
of London in 1950, M.Sc. in 1953 and later a Ph.D. in Chemistry from
the University of Glasgow. He did his postdoctoral research from 1956
through 1958 with Professor W. Libscomb in Minneapolis. Inspired by a
lecture by Dorothy Hodgkin to work on the determination of the crystal
structure of biological macromolecules, he returned to England to work
with Max Perutz on the structure of haemoglobin at the MRC during the
exciting years spanning from 1958 to 1964. From then on, his ideas,
programs, structures, and papers have had a tremendous influence in
the field of macromolecular crystallography.
He married a remarkable woman, Audrey Pearson, in 1954 and they
have three children (Alice, Martin, and Heather). Many old-timer
crystallographers will remember the very first `cartoon' sketches
of lactate dehydrogenase (LDH). Following Anders Liljas' suggestion,
they were drawn by Audrey to simplify the wanderings of the
polypeptide chain in space. Those drawings that today are so
commonplace in all kinds of colors, shades and hues, have their
origin in those crude hand-drawn diagrams. Incidently, she is
also a superb potter.
Some may wonder, why this sudden interest in recognizing
Professor M. G. Replacement. I must confess that his 65th birthday is
only partly the reason. The idea originated when I recently saw a paper
in one of the leading journals of our field where a structure had been
solved by phase refinement using electron density averaging and there
was no reference to Professor M. G. Replacement. At first, thinking
it was pretty sad, I decided to write this note. But then, on second
thought, I realized that in the end it may be of great honor to be
passed on into oblivion. Do we quote Sir Isaac Newton every time
we use the principle of inertia? Do we refer to the author of the
Principia every time we use any of his equations? Certainly not. His
work is all ingrained within the fabric of our science and our culture.
Similarly, the work of Professor M. G. Replacement is now, and for
evermore, part of the framework of macromolecular crystallography.
Taking some literary liberties, I would like to finish this brief
homage with an adaptation of a well known American folk song. I leave
it to the reader to find out the first and last names of
Professor M. G. Replacement, his favorite hobby (I already disclosed
the name of his wife and partner), and the name of the river that
crosses the city in Indiana were both have lived since 1964.
M... sail the boat ashore, Hallelujah
M... sail the boat ashore, Hallelujah
Audrey help to trim the sails, Hallelujah
Audrey help to trim the sails, Hallelujah
Wabash river is chilly and cold, Hallelujah
Freezes the body but not the soul, Hallelujah
Wabash river is deep and wide, Hallelujah
Milk and honey on the other side, Hallelujah
------------------------------------------------------------------------
CIF WORKSHOP AT 1995 ANNUAL ACA MEETING
This article was written by Philip Bourne, San Diego
Supercomputer Center (SDSC), San Diego, CA, USA.
The Crystallographic Information File (CIF) is a data representation
and exchange format commonly used in small molecule crystallography.
Most of the small molecule solution packages can produce CIF files,
a common form of submission for papers to Acta C.
With the availability of a macromolecular CIF (mmCIF) dictionary, a
powder diffraction dictionary, and other dictionaries currently in
progress (modulated structures, meta graphics, amino acid and
nucleotide properties, etc.), the need for a Workshop describing
these dictionaries and new software which uses them was considered
timely. The Workshop was sponsored by COMCIFs, the IUCr-appointed
committee which oversees the CIF standard, organized by Phil Bourne
from SDSC, and held during the 1995 Annual ACA Meeting held in
Montreal, Canada. Approximately forty people were in attendance.
Bourne opened the Workshop with a brief discussion on the history of
CIF and described how similar efforts are only now starting to emerge
in other disciplines. He emphasized the need for the crystallographic
community to recognize that the high level of formalized data
description achieved is presently unique among scientific disciplines.
This offers new opportunities for software development as well as
better access to a fast growing body of data through the use of
comprehensive databases.
Syd Hall (University of Western Australia), the founder of CIF,
elaborated on the history of the Self-defining Text Archival and
Retrieval (STAR) format from which CIF is derived as well as CIF
itself. STAR is a simple set of rules from which a Dictionary
Definition Language (DDL) can be derived. The DDL defines the form
of the various dictionaries and, as Hall pointed out, is critical
to the development of good software. He also described CIFtbx (CIF
Toolbox), a set of Fortran routines for the basic reading and writing
of CIF files (ftp site 130.95.232.12). He emphasized the need for
further software development particularly in the reading and browsing
of CIF files.
Brian McMahon (IUCr) provided insight into CIF processing at the
IUCr offices in Chester, and the software developed to process
CIF-based submissions to Acta C. Of the 582 submissions to Acta C
this year, 76 percent were CIF's that included the text of the paper.
Any submissions in hardcopy form are first turned into a CIF and all
submissions undergo data checking and subsequent format conversion
into an easily-read form. Once accepted, a paper may automatically
be converted into a final typeset version in the style of Acta C.
McMahon also reported on three recent developments of great benefit
to authors. First, is the availability of a booklet entitled `A Guide
to CIF for Authors.' Second, is the ability to submit a CIF file via
e-mail to checkcif@iucr.ac.uk. In return, the submitter will receive
a detailed report of errors and potential errors found. This includes
syntax errors, data items not conforming to the official dictionaries
(a potential error), missing data items, data items with unusual
values, derived values, and an indication that higher symmetry than
reported may exist. Once the entry has passed checkcif, the CIF can
be sent to printcif@iucr.ac.uk, the third recent development. Printcif
produces a PostScript-formatted version of the file with any problematic
values highlighted. This formatted version is not used by the journal,
but is easy to read and correct.
Paula Fitzgerald (Merck Sharp and Dohme Research), Chairperson of
the mmCIF Working Group, presented an overview of the mmCIF
dictionary and an update of recent progress. The current mmCIF
dictionary is composed of over 20,000 lines and contains a
description for several thousand data items organized into over
300 categories. The categories are further subdivided into groups
to provide a hierarchical representation which traces the progress
of the crystallographic experiment and the subsequent structure.
While the development of the dictionary took five years of volunteer
effort, it should be acknowledged that the dictionary is comprehensive
and provides very useful reference work. The draft mmCIF dictionary
is finished except for the incorporation of changes recognized by
the community and final editorial checking by COMCIFs. The current
draft dictionary can be found as an ASCII file at the WWW site
http://ndbserver.rutgers.edu/mmCIF or on PDB's WWW home page. Also
present are limited examples and introductory material. The contents of
the site will be expanded in the near future. A listserver has also
been established. To subscribe, send an e-mail message to
mmciflist@ndbserver.rutgers.edu containing the words: subscribe
mmciflist your-name. Version 1.0 of the dictionary will be available
within three to six months.
Eldon Ulrich (University of Wisconsin) described progress with the
NMR dictionary (NMRif). This project began at the April 10, 1994
Workshop, Biological Macromolecular NMR Data Exchange and Archiving,
organized by members of BioMagResBank and the mmCIF committee. The
CIF and mmCIF concept and its development was described to scientists
from the NMR community and proposed as a format for macromolecular NMR
data exchange. BioMagResBank, under the direction of Eldon Ulrich,
agreed to undertake the task of developing the dictionary with the
help and advice of volunteers from the NMR community. The dictionary
is represented as a relational database using a schema design tool
called Opossum. Development of the relational schema has been carried
out in collaboration with Miron Livny and Yannis Ioannidis, computer
scientists at the University of Wisconsin. The current dictionary
contains over 260 tables or categories comprised of more than 750
unique data names. While no estimate was given for the dictionary
completion date, it is expected to grow to double or triple its current
size. It was suggested that Opossum be used as a graphical tool for
representing and browsing the formidable mmCIF dictionary.
Gotzon Madariaga (University del Pais Vasco, Bilbao, Spain) presented
the main features of the modulated structures dictionary he is
developing, which is a superset of all the data items defined by
the Commission on Aperiodic Crystals. A draft of this dictionary has
been submitted to the IUCr. Interestingly, he raised several issues
relating to problems with CIF which had also been noted by the mmCIF
developers. Notable was the need to provide a reference between related
blocks of data possibly contained in different files. The lack of
nested loops in CIF (which are available in STAR) was also raised
because the lack of these loops makes it more cumbersome to represent
the data.
The final morning session was given by Bourne and concerned two
new dictionaries based on CIF. The first was a dictionary to
process abstracts for the ACA Meeting. Each of seventy CIF abstracts
was submitted either using a WWW form or by completing a template
form. The WWW form processing was automatic whereas many of the
templates had to be hand-edited. Bourne concluded that since it
was not necessary to collect statistics on the CIF submissions,
processing them was more effort than was warranted. The second
dictionary is a meta graphics (mg) dictionary to facilitate data
exchange between graphics programs. The mg dictionary, while
preliminary, is designed to capture all the salient features seen
in the display of a macromolecule such that the biological
structure/function visualized in the graphics representation are
preserved and can be loaded into a variety of graphics programs. A
long-term advantage of this approach is that graphics images are
easily stored in a database and can be extracted as needed.
Vivian Stojanoff (Brookhaven National Laboratory) began the afternoon
session with a discussion of an extension to the mmCIF dictionary for
representing structure factors. While the current structure dictionary
is not considered complete, it does describe more than the basic
h,k,l,F and sigmaF found in many existing PDB submissions. Currently
there is support for data from multiple derivatives and wavelengths.
John Westbrook (Rutgers University) described the Dictionary
Definition Language (DDL) he developed in response to the needs of
the macromolecular dictionary. The current small molecule core
dictionary uses DDL version 1.4. Westbrook developed version 2.1
which is upwardly compatible with version 1.4 but is much more
rigorous. While this has little significance to the crystallographer,
it is important to the software developer who needs a consistent way
of representing both dictionaries and data files so that one piece of
software can be used on both. Version 2.1 of the DDL offers that
opportunity.
Syd Hall returned to describe the program Xtal_GX which provides a
general approach to processing CIFs and uses the CIFtbx he described
earlier in the day. It also has a graphics feature for display
purposes.
The final formal presentation was given by Weider Chang (Columbia
University) who described the next-generation, object-oriented tools
he is developing with Bourne for basic CIF manipulation. Chang
presented the basic layout of the library which is written in
Objective C and from which browsers, a CIF2HTML convertor, and
several dictionary checking tools have been developed. The CIF2HTML
convertor was used in the ACA abstract procedure.
A lively discussion followed the formal presentations pertaining to
the need of recognizing which subset of mmCIF data items will
constitute a formal PDB entry. Attendees seemed well satisfied
with the workshop - perhaps it will lead to development of other
dictionaries as well as new, useful software.
BROOKHAVEN ORDER FORM
Name of User __________________________________ Date _________
Organization __________________________________ Phone _________
Address __________________________________ Fax _________
__________________________________ E-mail _________
__________________________________
--------------------------------------------------------------------------
- Price is valid through September 30, 1996
- Price is per CD-ROM set released - releases occur four times per year
- Facsimile and phone orders are not acceptable
--------------------------------------------------------------------------
The Protein Data Bank MUST receive all three of the following items
before shipment can be completed (please send all required items
together via postal mail - facsimile and phone orders are NOT acceptable):
1. Completed order form;
2. Mailing label indicating exact shipping address;
3. Payment (using one of the two options below):
- Check payable to Brookhaven National Laboratory in U.S. dollars and drawn
on a U.S. bank. Foreign checks cannot be accepted and will be returned.
- Original purchase order payable to Brookhaven National Laboratory. After
your order is processed, you will be invoiced by Brookhaven National
Laboratory. Please indicate exact address invoice should be sent to:
________________________________________
________________________________________
________________________________________
A wire transfer is acceptable only AFTER we have received an original purchase
order from your organization and you have been invoiced by Brookhaven. After
receiving Brookhaven's invoice, your bank may send a wire transfer to:
Bank name : Morgan Guaranty Trust Co. of New York
Account name : Brookhaven National Laboratory
Account number : 076-51-912
Please send all three required items together via postal mail to:
Protein Data Bank Orders
Chemistry Department, Building 555
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000 USA
------------------------------------------------------------------------
1 Protein Data Bank CD-ROM Set - ISO 9660 Format $332.26
(tax and shipping charges not applicable)
------------------------------------------------------------------------
AFFILIATED CENTERS
Twenty-two affiliated centers offer DATAPRTP information for distribution.
These centers are members of the Protein Data Bank Service Association
(PDBSA). Centers designated with an asterisk(*) may distribute DATAPRTP
information both on-line and on magnetic or optical media; those without
an asterisk are on-line distributors only.
BMERC
BioMolecular Engineering Research Center
College of Engineering, Boston University
Boston, Massachusetts
Nancy Sands (617-353-7123)
sands@darwin.bu.edu
http://bmerc-www.bu.edu/
*BIOSYM
BIOSYM Technologies, Inc.
San Diego, California
Rick Lee (619-546-5536)
rickl@biosym.com
http://www.biosym.com/
BIRKBECK
Crystallography Department
Birkbeck College, University of London
London, United Kingdom
Alan Mills (44-171-6316810)
a.mills@cryst.bbk.ac.uk
http://www.cryst.bbk.ac.uk/PDB/pdb.html/
CAN/SND
Canadian Scientific Numeric Data Base Service
Ottawa, Ontario, Canada
Roger Gough (613-993-3294)
cansnd@vm.nrc.ca
CAOS/CAMM
Dutch National Facility for Computer Assisted Chemistry
Nijmegen, The Netherlands
Jan Noordik (31-80-653386)
noordik@caos.caos.kun.nl
http://www.caos.kun.nl/
*CCDC
Cambridge Crystallographic Data Centre
Cambridge, United Kingdom
David Watson (44-1223-336394)
watson@chemcrys.cam.ac.uk
CSC
CSC Scientific Computing Ltd.
Espoo, Finland
Heikki Lehvaslaiho (358-0-457-2076)
heikki.lehvaslaiho@csc.fi
http://www.csc.fi/
CINECA
NE Italy Interuniversity Computing Center
Casalecchio di Reno (BO), Italy
Laura Setti (39-51-6599478)
asltc0@icineca.cineca.it
ICGEB
International Centre for Genetic Engineering and Biotechnology
Trieste, Italy
Sandor Pongor (39-40-3757300)
pongor@icgeb.trieste.it
EMBL
European Molecular Biology Laboratory
Heidelberg, Germany
Hans Doebbeling (49-6221-387-247)
hans.doebbeling@embl-heidelberg.de
http://www.EMBL-Heidelberg.DE/
INN
Israeli National Node
Weizmann Institute of Science
Rehovot, Israel
Leon Esterman (972-8-343934)
lsestern@weizmann.weizmann.ac.il
*JAICI
Japan Association for International Chemical Information
Tokyo, Japan
Hideaki Chihara (81-3-5978-3608)
*MAG
Molecular Applications Group
Palo Alto, California
Hilary Jensen (415-473-3039)
hilary@suerte.mag.com
http://hyper.stanford.edu/~Mag/
*MSI
Molecular Simulations Inc.
Burlington, Massachusetts
Lance J. Ransom Wright (617-229-9800)
lance@msi.com
http://www.msi.com/
NCHC
National Center for High-Performance Computing
Hsinchu, Taiwan, ROC
Jyh-Shyong Ho (886-35-776085; ex: 342)
c00jsh00@nchc.gov.tw
NCSA
National Center for Supercomputing Applications
University of Illinois at Urbana-Champaign
Champaign, Illinois
Patricia Carlson (217-244-0768)
pcarlson@ncsa.uiuc.edu
NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION
National Library of Medicine
National Institutes of Health
Bethesda, Maryland
Stephen Bryant (301-496-2475)
bryant@ncbi.nlm.nih.gov
http://www.ncbi.nlm.nih.gov/
*OML
Oxford Molecular Ltd.
Oxford, United Kingdom
Steve Gardner (44-1865-784600)
sgardner@oxmol.co.uk
http://www.oxmol.co.uk/
*OSAKA UNIVERSITY
Institute for Protein Research
Osaka, Japan
Yoshiki Matsuura (81-6-879-8605)
matsuura@protein.osaka-u.ac.jp
PITTSBURGH SUPERCOMPUTING CENTER
Pittsburgh, Pennsylvania
Hugh Nicholas (412-268-4960)
nicholas@psc.edu
http://pscinfo.psc.edu/biomed/biomed.html/
SEQNET
Daresbury Laboratory
Warrington, United Kingdom
User Interface Group (44-1925-603351)
uig@daresbury.ac.uk
*TRIPOS
Tripos, Inc.
St. Louis, Missouri
Akbar Nayeem (314-647-1099; ex: 3224)
akbar@tripos.com
------------------------------------------------------------------------
Protein Data Bank
Chemistry Department, Bldg. 555
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000 USA
------------------------------------------------------------------------
TO CONTACT PDB
Telephone 516-282-3629
Facsimile 516-282-5751
Internet:
pdb@bnl.gov.....................general correspondence
orders@pdb.pdb.bnl.gov..........order information
sysadmin@pdb.pdb.bnl.gov........network services
listserv@pdb.pdb.bnl.gov........Listserver subscriptions
pdb-l@pdb.pdb.bnl.gov...........Listserver postings
errata@pdb.pdb.bnl.gov..........entry error reporting
Please include your name, postal mailing address, e-mail address,
facsimile number, and telephone number in all correspondence.
------------------------------------------------------------------------
INTERNET SITES
WWW.....................http://www.pdb.bnl.gov
FTP (anonymous).........ftp.pdb.bnl.gov
Gopher..................gopher.pdb.bnl.gov
------------------------------------------------------------------------
STATEMENT OF SUPPORT
PDB is supported by a combination of Federal Government Agency
funds (work supported by the U.S. National Science Foundation;
the U.S. Public Health Service, National Institutes of Health,
National Center for Research Resources, National Institute of
General Medical Sciences, and National Library of Medicine; and
the U.S. Department of Energy under contract DE-AC02-76CH00016)
and user fees.
------------------------------------------------------------------------
PDB STAFF
Joel L. Sussman, Head
David R. Stampf, Sr. Project Mgr.
Enrique E. Abola, Science Coordinator
Jaime Prilusky, Interim Head Database Dev.
Frances C. Bernstein
Judith A. Callaway
Minette Cummings
Betty R. Deroski
Pamela A. Esposito
Arthur Forman
Patricia A. Langdon
Michael D. Libeson
Nancy O. Manning
John E. McCarthy
Regina K. Shea
Janet L. Sikora
Karen E. Smith
Dejun Xue
------------------------------------------------------------------------
------------------------------------------------------------------------