**** **** **** * * * * * * **** **** **** * * * * * * **** **** * * **** HEADLINES - a digital monthly publication
Contents of This Issue:
1. NEWS FLASH - SSRL Named as Part of a Major New Center for Structural
Genomics Activity
(contact: Peter Kuhn, kuhn@ssrl.slac.stanford.edu)
On Tuesday, September 26, 2000, the NIH National Institutes of Health
Institute of General Medical Sciences (http://www.nigms.nih.gov) announced the
funding of seven new centers for structural genomics. SSRL, in partnership with
The Scripps Research Institute/Genomics Institute for the Novartis Research
Foundation and the University of California, San Diego/San Diego Supercomputer
Center, formed the Joint Center for Structural Genomics (JCSG, http://www.jcsg.org),
which will be one of the new centers. The grant of ~$24 million over a five-year
period will be focused on the goal of determining the novel three- dimensional
structures of up to 2000 proteins by developing state-of-the- art
high-throughput technology, thereby advancing efforts to understand
structure-function relationships important for diseases and their treatments.
JCSG is organized around three collaborative teams and includes 29 outside
collaborators from the United States, Europe and Japan. The bioinformatics team
directs target selection, informatics, and validation; the crystallomics team is
responsible for production of protein samples and crystallization; the structure
determination team (headed by Peter Kuhn of SSRL), orchestrates x-ray data
collection and analysis, structure determination, and refinement. The
developments in robotics, beam line automation and control, data analysis,
structure solution and refinement already ongoing at SSRL with funding from NIH-
NCRR (http://www.ncrr.nih.gov) and DOE-BER
(http://www.er.doe.gov/
production/ober/ober_top.html)
will form the basis of core technologies important for the success of the JCSG
high-throughput structure determination pipeline. Synchrotron beam time for JCSG
will be provided through additional new capacity being developed at SSRL and
through a beam line at ALS funded by the Genomics Institute of the Novarits
Research Foundation (where new robotics technologies are also being
developed).
2. SSRL Staff Contributes Significantly to International Conference - SRI2000
(contact: Piero Pianetta, pianetta@ssrl.slac.stanford.edu)
This year's International Conference on Synchrotron Radiation Instrumentation
(SRI2000), held in Berlin, Germany this past August, clearly illustrated the
dynamic nature of synchrotron radiation research with over 700 attendees
exchanging information on a very diverse set of topics. SSRL staff and
scientists made a number of important oral contributions at the meeting. Jo
Stohr gave the opening plenary lecture on "The Power of X-ray Polarization:
From Spectroscopy to Microscopy", illustrating how the unique combination
of elemental specificity, chemical specificity and polarization control afforded
by synchrotron- based x-ray spectroscopy and microscopy has led to important
scientific discoveries in forefront areas of materials science. Piero Pianetta
gave a presentation on "Recent Advances in Synchrotron Radiation TXRF"
(as well as a talk at the satellite conference on Metrology with Synchrotron
Radiation held in association with SRI2000). Pavel Petrashen presented some of
his recent work in a talk on "Graded SiGe Crystals as X-ray
Collimators". Peter Kuhn described the approaches being developed at SSRL
for high-throughput structural genomics within the framework of the
macromolecular crystallography program (see item #1). Roman Tatchyn discussed
work related to the next generation light source (LSLC) in a talk titled
"Overview of the Radiation Characteristics of the LCLS." An SSRL
facility poster was on display throughout the conference and SSRL also
contributed to and prepared the facility poster on SESAME. Overall, the
conference emphasized the opportunities that could be derived from the new third
generation sources including microbeams, coherence and variable polarization. A
session on fourth generation sources showed how these capabilities could be
further extended with x-ray free electron lasers. The next instrumentation
conference, the eighth in the series, will be held in San Francisco in 2003 and
hosted jointly by the ALS and SSRL (see #5).
3. SSRL 27th Annual Users' Meeting/Workshops -NOTE They are Coming Soon!
(contacts: Lisa Dunn, lisa@ssrl.slac.stanford.edu;
Michelle Steger, steger@ssrl.slac.stanford.edu)
With the Users' Meeting less than a month away, several deadlines are fast approaching. September 29 is the deadline for early registration, October 2 for submitting nominations for the Farrel Lytle Award and October 8 for poster abstract submissions. (Please note: space and inclusion in program materials cannot be guaranteed for poster submissions after October 8.) Five workshops will be held in conjunction with this upcoming meeting:
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For more detailed information regarding the 2000 Users' Meeting and
workshops, including draft programs, registration information, poster submittal,
the Lytle award and SSRLUO-EC voting updates see: http://www-ssrl.slac.stanford.edu/conferences/ssrl27/
4. Summer Shutdown Update - Wrapping up a Big Job with Success
(contact: Piero Pianetta,
pianetta@ssrl.slac.stanford.edu)
A major reconstruction of parts of the SPEAR tunnel and alcoves has been successfully completed in preparation for the SPEAR3 installation. After the new 24,000 lb. concrete rolling door for the Beam Line 2 alcove area was installed and the rest of the heavy construction activities were completed a couple of weeks ago, a thick layer of dust covered the SPEAR parking lot, nearby buildings and plastic-shrouded beam lines alike, creating an unnerving picture. Rest assured, this picture did not last long as SSRL staff are currently involved in a full-scale effort to clean -up after the construction, complete various shutdown projects and reinstall Beam Line 2 components, including a new mirror tank, LCW, PPS, MPS and hutch tables, in time for the startup clock to start ticking on October 4. A number of other shutdown projects, which will ultimately benefit user operations, have already been completed or are currently underway including:
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SPEAR will soon be prepared for first beam and the start of the 2000 user run
(see #10 below).
5. SSRL and ALS to co-Host SRI 2003 in San Francisco
(contact: Jo Stohr, stohr@ssrl.slac.stanford.edu)
The 2003 International Conference on Synchrotron Radiation Instrumentation
(SRI 2003) will be held in San Francisco and hosted jointly by SSRL and the ALS.
The site proposal was presented last month in Berlin at SRI 2000 and accepted by
the International SRI Advisory Committee, consisting of the Directors of world's
synchrotron radiation facilities. Howard Padmore (ALS) and Jo Stohr (SSRL) will
be the conference co-chairs. SRI 2003 is expected to draw more than 600
attendees and is one of the largest and most important synchrotron- related
meetings in the world. The conference will take place at an exciting time for
the host facilities with the availability of the superbends at the ALS and the
completion of the SPEAR3 upgrade at SSRL. It is even hoped that in 2003
construction will have started on the first x-ray free electron laser in the
world, the Linac Coherent Light Source (LCLS), which uses the last third of the
linac at SLAC. The conference will consist of selected plenary talks on
forefront scientific topics and numerous invited and contributed talks on
instrumentation associated with synchrotron and free electron laser facilities.
The conference is tentatively scheduled for August 2003.
6. SSRL to Host XAFS XIII in 2006
(contact: Britt Hedman, hedman@ssrl.slac.stanford.edu)
SSRL has been chosen to host the 13th International Conference on X-ray
Absorption Fine Structure (XAFX XIII). The meeting will be held on the Stanford
campus in the Summer of 2006. The selection was made by the International XAFS
Society Executive Committee at their meeting held in conjunction with the XAFS
XI Conference in Ako, Japan in late July of this year. The conference is held
every three years (the 2003 site is MAX-lab, Lund Sweden), and focuses on the
most recent developments in theory and experimental methods, as well as
applications in a variety of scientific fields, including materials science,
physics, chemistry, biology and medicine. This year's conference in Japan was
attended by around 500 participants. This is a return for this conference to
SSRL - it was held here in the summer of 1984.
7. SMB Summer School 2000: Making the Most of Your Synchrotron Trip - a
Training Success
(contacts: Ana Gonzalez, agonzalez@ssrl.slac.stanford.edu,
Ashley Deacon - ash@smb.slac.stanford.edu,
Peter Kuhn - kuhn@ssrl.slac.stanford.edu)
The first SSRL SMB Summer School, supported by the NIH NCRR as a component of
the training activity of SSRL's center grant, and by corporate sponsors
including Agouron, Compaq, SGI, ADSC and CCP4, was held last week (September
19-23). The school was organized into a series of morning lectures primarily
focussing on state-of-the-art macromolecular crystallography techniques, open to
registered and non- registered participants alike, and practical, hands-on
tutorials for a group of 26 registered student participants in the afternoons.
The participants represented a large number of the user groups utilizing SSRL
for their macromolecular research. The afternoon lectures/tutorials were geared
to provide the students with intensive training in sample preparation, data
collection and structure determination. In addition to the SSRL SMB staff (see
agenda url below), tutorials on the various topics were given by Bill Weis
(Stanford), Elspeth Garman (University of Oxford), Andrew Leslie and Phil Evans
(University of Cambridge), Thomas Schneider (University of Goettingen), Duncan
McRee (TSRI), Eleanor Dodson (University of York), Paul Adams (CCI, LBNL),
Thomas Terwilliger (LANL) and Anastassis Perrakis (EMBL Grenoble). Graeme Laver
(The Australian National University) gave a special evening keynote lecture on
"Adventures with the Flu". The School seemed a great success for
students and tutors alike with much being learned and information exchanged. A
SMB Summer School will become an annual event at SSRL. For further information,
see http://smb.slac.stanford.edu/summer_school/
8. Structural Molecular Biology Software
Development Workshop
(contacts: Tim
McPhillips, tim@ssrl.slac.stanford.edu;
Peter Kuhn, kuhn@ssrl.stanford.edu)
SSRL also held a Structural Molecular Biology Software Development Workshop
on September 18 in conjunction with the SMB Summer School. Developers of
structural biology software applications in the macromolecular crystallography
area were invited to attend the workshop and give presentations (regardless of
whether they were involved in the Summer School). The workshop was organized
around several topical headings: software process, distributed computing,
programming languages, GUIs, database technology, and collaboratories in
crystallography. The workshop was formatted such that the morning session was
devoted to talks on software development methodologies and the afternoon session
to the actual projects themselves. Presentations and discussions focused on the
design of an advanced software framework as required for modern sophisticated
structure determination and analysis. For further information see http://smb.slac.stanford.edu/summer_school/software_workshop/.
9. Additional Press on Science Paper on HK97 Virus
(contact: Hiro Tsuruta, tsuruta@ssrl.slac.stanford.edu)
A paper on "Topologically Linked Protein Rings in the Bacteriophage HK97
Capsid" by William R. Wikoff (TSRI), Lars Liljas (TSRI/U. of Uppsala),
Robert L. Duda (U. of Pittsburgh), Hiro Tsuruta (SSRL), Roger W. Hendrix (U. of
Pittsburgh) and John E. Johnson (TSRI) appearing in the September 22 issue of
Science has received some additional press both locally in the Stanford Report (http://www.stanford.edu/dept/news/report/news/september27/virus-920.html) and
internationally in a National Tokyo edition of Mainichi, a Japanese newspaper
with a distribution comparable to the Los Angeles Times. The Science paper
reported the 3.6-A resolution crystal structure of the Hong Kong 97
bacteriophage mature empty capsid, which is the first double-strand DNA virus
whose crystal structure has been solved. A low-resolution single crystal
diffraction data set recorded on BL4-2 was essential in solving the diffraction
phase problem. This study revealed the topological linkage of polypeptide chains
in a way similar to chain mail suits worn by medieval knights to stabilize the
very thin phage capsid (18 A thick compared to the 660 A diameter) for the first
time.
10. Information on 2000 Run and Beam Time Schedule
(contact: Lisa Dunn, lisa@ssrl.slac.stanford.edu)
The run schedule for the initial third of the FY01 SSRL run is very close to complete, and beam time assignments will be distributed to the spokespersons by October 1. We also wish to remind our users, as mentioned in the August issue of HEADLINES, that the Fall deadline for submission of beam time proposals has been moved from October 1 to November 1 (does NOT apply for macromolecular crystallography proposals - they are due December 1).
SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site: http://www-ssrl.slac.stanford.edu/
You can subscribe or remove your name from the distribution list by sending a brief email with your request to Lisa Dunn, editor, at lisa@ssrl.slac.stanford.edu.
