Recently in general announcements Category
A manuscript highlighting the technical capabilities of the SIBYLS beamline has been published in the Journal of Applied Crystallography:
The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world’s mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B4C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.
Hello DOMO users,
DOMO is fairly robust, and is capable of handling your precious crystals mounted in a variety of bases:
However, you must take some care when gluing or epoxying the pins into the bases. If there is too much glue or epoxy or you inadvertantly get some on the sides or bottom of the base this will cause the robot to jam, which will require time-wasting reset procedures, lost samples, and unhappy beamline support personnel.
Here is a recent example of several pins where the user (who will remain unnamed) applied entirely too much epoxy. Somehow the user was able to load these pins into the cassette, but they caused the robot to jam.
There are more detailed tips and hints on the SSRL SMB website for preparing your bases and pins.
Summary of Options for Applying for Beamtime at the ALS
RAPIDD - a rapid access process, replaces the 2-month proposal system. SAXS proposals should use the RAPIDD system. MX applicants may apply for either RAPIDD or 6 Month Proposals.
The aim is to provide quick turnaround. Proposals are fairly simple, requiring a one page pdf describing the science, and will be accepted at any time. Proposals are sent out for review within two business days, and we hope to complete the review within 2-3 weeks. Beamtime may be allocated at any time after submission depending on your proposal score, the number of proposals submitted, and the beamtime available. We have never rejected a RAPIDD application for SAXS data collection except for applications proposing technically impossible experiments nto suited to the SIBYLS beamline.
This mechanism will suit regular long-term users of the ALS. It has been available since January 2012 and 14 research groups successfully established a 2-year research program in the first cycle. The mechanism allows users to apply for a longer term program through the regular ALS proposal cycle. Proposals are accepted every 6 months, for beamtime starting 4 months later. These proposals may be renewed for subsequent 6 month cycles for up to 2 years. Proposals may cover a broad program of work, and will be submitted as a PDF file, up to 3 pages long. We hope this will reduce the overall workload for users who currently submit more than one proposal a year.
3rd annual SIBYLS bioSAXS workshop is ON !!
Date: October 9-10, 2012 Location: Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA
The SIBYLS team will host a workshop with strong emphasis on experimental aspects of Small Angle X-ray Scattering techniques in structural biology. The two-day workshop will provide training on experimental techniques and software tutorial sessions primarily for biological SAXS studies. One day of the workshop will be dedicated for data processing by workshop participants. The latest advances in SAXS studies on biological systems will be reported and discussed by several experts in a diverse spectrum of structural biology benefiting from bioSAXS (see program bellow). Also planned are presentations on complementary experimental approaches (MODELLER) and solution structure modeling techniques using ensemble analysis. Participants will receive updates on current developments at SIBYLS and development of software dedicated to analyze SAXS for structural biology.
Enrollment is limited to 30 participants.
Organizers: Michal Hammel, Greg Hura, Robert Rambo
Inquires: Jane Tanamachi
Registration: To attend "Course on SAXS" you need register for the 2012 Advanced Light Source Users' Meeting. ALS user meeting will be held at Berkeley Lab beginning Monday, October 8. "Practical Course on SAXS" will begin Thuesday October 9th and continue through Wednesday October 10th. When you registering, you must indicate "SIBYLS bioSAXS"
Tuesday, October 9th LBNL ( B50 Auditorium )
11:30 Lunch at the ALS patio
12:40 Welcoming Remarks Michal Hammel
12:45 Robert Rambo, LBNL, Berkeley "Small-Angle Scattering and its Application to Soft matter Science: Historical Remarks" "New ways to analyze SAXS from biological material"
13:25 Greg Hura, LBNL, Berkeley "SIBYLS SAXS capabilities and future developments
15:10 Coffee Break
15:20 Alex Grishaev, NIH Title: TBD
16:00 Patrick Weinkam , UCSF "Conformational Sampling to predict SAXS profile: How to use MODELLER"
16:30 Gareth Williams, LBNL "SAXS combined with crystallography and computation: Application of the Ensemble Analysis "
17:00 Michal Hammel , LBNL "Resolution in SAXS"
Wednesday, October 10th LBNL ( B50 Auditorium ),
9:00 Rob Rambo, LBNL, Berkeley "Scatter: New software for SAXS data processing"
9:50 Michal Hammel, LBNL, Berkeley "FOXS-MES-MODELLER: New software for solution structure modeling"
10:30 Coffee Break
10:45 Greg Hura, Robert Rambo and Michal Hammel, LBNL, Berkeley "Data reduction and processing tutorial"
12:00 Lunch Break at the ALS patio
Practical session with Mentors (Greg Hura, Rob Rambo and Michal Hammel)
13:00-17:00 Participating Students "Practical Session - Data reduction and processing"
* Course on SAXS from Biological Material*
Date: October 4-5, 2011 Location: Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA
The significance of Small Angle X-ray Scattering (SAXS) technique has been rediscovered in recent years by an increasing number of structural biologists to complement high resolution structural studies by crystallography, EM and NMR. SIBYLS team will host workshop with strong emphasis on experimental aspects of non-crystalline diffraction techniques in biology. The two-day workshop will provide training on experimental techniques and software tutorial sessions primarily for biological SAXS studies. One day workshop will be dedicated for data processing by workshop participants. The latest advances in SAXS studies on biological systems will be reported and discussed by several experts in a diverse spectrum of structural biology benefiting from non-crystalline diffraction studies (see program bellow). Also planned are presentations on complementary experimental approaches and modeling techniques. Participants will receive updates on current developments at SIBYLS and development in the software dedicated to analyze SAXS for structural biology.
Due to the limited space availability only first 40 registered participants will be accepted.
Organizers: Michal Hammel, Greg Hura
Inquires: Jane Tanamachi JTanamachi@lbl.gov
Registration: To attend “Course on SAXS” you need register for the 2010 Advanced Light Source Users’ Meeting. ALS user meeting will be held at Berkeley Lab beginning Monday, October 3. “Practical Course on SAXS” will begin Thuesday October 4th and continue through Wednesday October 5. When you registering, you must indicate “Course on SAXS from Biological Materials” . Registration Fee: The early registration fee is $225.00 (regular) and $95.00 (student); after Friday, September 24, the registration fee will be $250.00 (regular) and $115.00 (student).
Tuesday, October 4th LBNL (room 54-130-Pers. Hall)
12:45 Welcoming Remarks Michal Hammel
12:50 Robert Rambo, LBNL, Berkeley “Small-Angle Scattering and its Application to Soft matter Science: Historical Remarks” “New ways to analyze SAXS from biological material”
13:50 Greg Hura, LBNL, Berkeley
“SIBYLS SAXS capabilities and future developments
15:00 Coffee Break
15:15 Stefan Arold UCSF, The University of Texas, Housten “SAXS as a tool to study multi-domain proteins and protein multimerisation “
15:45 Alexei Kazantsev, UC Boulder, Colorado “RNase P RNA: from pieces of the crystal structure to the complete structure in solution. “
16:15 Alexander Johs, Oak Ridge National Laboratory, Oak Ridge “SAXS reveals the intramolecular metal ion transfer between flexibly-linked domains of mercuric ion reductase”
16:45 Jack Tanner, University of Missouri-Columbia, Columbia , “SAXS Studies of the Quaternary Structures of Proline Utilization A (PutA) Proteins”
Wednesday, October 5th LBNL (room 54-130-Pers. Hall),
9:00 Michal Hammel, LBNL, Berkeley “Criteria for evaluation of SAXS results”
9:30 Rob Rambo, LBNL, Berkeley “OPTIMUS: New software for SAXS data processing”
10:00 Dina Schneidman UCSF, San Francisco ” SAXS software in Integrative Modeling Platform (IMP) and Chimera Interface “
10:30 Coffee Break
10:45 Greg Hura, Robert Rambo and Michal Hammel, LBNL, Berkeley “Data reduction and processing tutorial”
12:00 Lunch Break
13:00-16:00 Participating Students “Practical Session - Data reduction and processing”
We have been operating our SAXS mail-in/hand-in program for 6 months - 3 cycles of ALS proposals. The beamline and its staff are dedicated to developing and applying technologies and methodologies which combine SAXS and crystallography. Interacting with an extensive and robust external user community is a critical component of this development. Our mission for the mail-in/hand-in program is to provide SAXS data to users at as high or higher quality than if users were to come to the beamline and collect these data sets themselves. We believe this is possible since the data collection is now fast and the beamline interface has grown necessarily complex. Beamline staff which develop the interface are more likely to optimize data collection and spot problems earlier than most users. We initiated this program as we were no longer able to meet the growing demand for beamtime with all users coming on-site for data collection. Most users who participated in this program would not have been able to collect data at SIBYLS were it not for the mail-in/hand-in program.
We have conducted a survey of labs that have used the modality of SIBYLS to provide feedback - which we take very seriously. This should help inform new interested labs on how the system works. In addition we will compare input from future surveys against this one as a measure of progress. The number of labs which have gained access to SAXS data collection at SIBYLS has increased 10-fold.
We have significant room to grow and improve the system as highlighted by several users in our survey. Aside from developing the infrastructure for trouble free collection, a challenge is balancing the most easily implemented one size fits all approach with some user adjustablility. We hope to incorporate more flexibility for users as we develop. While the system has not been entirely trouble free - given the programs novelty, we are pleased with the feedback and encouraged that the mail-in/hand-in program is usefully continued. For example most users indicated they would use the mail-in/hand-in system again and a substantial number have papers in preparation based on data collected at the beamline. The survey and its results can be viewed by clicking the link below.
To free up space on the primary /data volume we’ve recently created compressed read-only archival filesystems (using the squashfs filesystem if you’re interested) for all MX and SAXS data collected at the SIBYLS beamline between 2007 and 2009. You will find the archives mounted as /2007_data, /2008_data, and /2009_data on most of the beamline computers. The MX ADSC *.img files which take up the bulk of the space have been moved from /data to the archival volumes, but the SAXS *.mccd files have only been copied to the archival system.