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We are pleased to announce the 5th annual SIBYLS bioSAXS workshop “Frontiers in biological SAXS”

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Date: October 7-8, 2014 Location: Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA

Small angle scattering (SAS) is experiencing a dramatic increase in popularity within the structural biology community. The availability of synchrotron radiation, low-noise detectors, powerful computing hardware, and better algoritms, has made the technique accessible to a much larger audience than ever before. At the same time, biologists are investigating ever more complex systems that pose increasing challenges to conventional crystallography. The latest advances in SAXS studies on biological systems will be reported and discussed in 2 days workshop by invited experts with focus on following four topics (see program). 1) Advances in Synchrotron Scattering technique 2) Dynamic & Flexible Structures in Biomolecules 3) Membrane Protein Scattering 4) Complementary Methods in Crystals and in Solution

The two-day workshop will provide training on experimental techniques and software tutorial sessions primarily for biological SAXS studies. Participants will also receive updates on current development of software dedicated to analyze SAXS for structural biology. Half day of the workshop will be dedicated for data processing by workshop participants. Enrollment is limited to 30 participants. 



Organizers: Michal Hammel, Greg Hura



Inquires: Jane Tanamachi

Registration: To attend “Frontiers in biological SAXS” you need register for the 2014 Advanced Light Source Users’ Meeting. ALS user meeting will be held at Berkeley Lab beginning Monday, October 6. “Frontiers in biological SAXS” will begin Thuesday October 7th and continue through Wednesday October 8th. When you registering, you must indicate “Frontiers in biological SAXS”

Tuesday, October 7th LBNL

11:30 Lunch at the ALS patio

12:30 Welcoming Remarks Michal Hammel and Greg Hura “Frontiers in biological SAXS”

12:45 Lois Pollack, Cornell Univesity

13:15 Edward Snell, Hauptman-Woodward Institute

13:45 Lokesh Gakhar, University of Iowa

14:15 Coffee Break

14:30 Greg Hura, LBNL

15:00 Dina Schneidman, University California, San Francisco “SAXS based modelling of proteins with long disordered fragments”

15:30 Sherry Wang, National Cheng Kung University, Taiwan “Molecular architecture and stepwise assembly of IL-33 signaling complex”

16:00 Yun-Xing Wang, (NIH/NCI)

16:30 TBD

17:00 TBD

Wednesday, October 8th LBNL

9:00 Michal Hammel, LBNL

9:30 Kevin Dyear, LBNL

10:00 TBD

10:30 Coffee Break

10:45 Greg Hura, and Michal Hammel, LBNL, Berkeley “Data reduction and processing tutorial”

12:00 Lunch Break at the ALS patio

13:00 - till late Practical session with Mentors (Greg Hura, Michal Hammel, Dina Schneidman, Kevin Dyer)

Young researchers are encouraged to apply for the Cancun conference “Dynamic Structures in DNA Damage Responses and Cancer” from the 12-15th February, 2014. We expect that there will be lively discussions on both methods and results during the sessions and good opportunities to interact with top colleagues. To inspire your productive discussions the conference venue has breath taking views of the Caribbean Sea and a great beach to enjoy with colleagues. There are a few spots to join the conference and some for late breaking talks so if you or your group members would appreciate this intimate and informative meeting on dynamic structures in DNA damage responses and cancer, then we would encourage you to APPLY. We are putting together many of the people driving advances under one roof to make this a meeting that will prove uniquely productive and informative for those working in this area and seeking collaborators. Although you may have a busy schedule we aim to make this meeting worth your taking the time to participate by directly aiding research progress and collaborations.

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.

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Classen, S, Hura, GL, Holton, JM, Rambo, RP, Rodic, I, McGuire, PJ, Dyer, K, Hammel, M, Meigs, G, Frankel, KA, and Tainer, JA “Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.” (2013). J Appl Crystallogr 46, 1-13.

Keeping DOMO happy

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Hello DOMO users,

DOMO is fairly robust, and is capable of handling your precious crystals mounted in a variety of bases:

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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.

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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

  1. 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.

  2. 6 MONTH PROPOSAL

    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 !!

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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*

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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).

PROGRAM

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),

Tutorial session,

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”

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