Recently in software Category

Date: May 9th 2019

Location: Advanced Light Source at Lawrence Berkeley National Laboratory, Berkeley, CA

Building 6, conference room #2202

SAXS_board.JPG This one-day workshop for current and future SIBYLS users will provide participants with software tutorial sessions for biological SAXS. The latest advances in SAXS studies on biological systems will be discussed with particular focus on advances in synchrotron scattering techniques, modeling of dynamic and flexible structures, and integrating bioSAXS analysis within high resolution structures.
Updates on current developments of software for SAXS analysis pertaining to structural biology will be reviewed.

We will begin with a brief run-through on current updates. Greg Hura, Berkeley Lab’s SAXS Beamline Scientist will introduce the future of high throughput. Michal Hammel, another one of Berkeley Lab’s SAXS Beamline Scientists, will present current developments in size exclusion chromatography coupled SAXS (SEC-SAXS) and give a talk about integrating high-resolution models in the SAXS modeling. Students and postdocs are encouraged to bring their own SAXS data collected at SIBYLS. We will provide an opportunity for participants to present and discuss their projects with the group. If you are interested in discussing your SAXS project, please email Kathryn Burnett. This will provide for a flux of ideas among workshop participants, and inspire new perspectives for future data analysis. During the afternoon session we will provide practical hands-on exercises with experts in SAXS software for data processing (SCATTER, FrameSlice and RAW, SAXS similarity maps, modeling tools (FOXS - MultiFoXS, BILBOMD and SAXS shape calculator).

Organizers: SIBYLS



Inquires: Kathryn Burnett

Limited to 30 participants.

Registration: Registration is now open. To attend the workshop you need to send an email to Kathryn Burnett

Lunch is provided.

SCHEDULE :

May 9, 2019 12:00 pm - 5:00 pm

Building 6, conference room #2202

12:00 - 1:30 pm Greg Hura and Michal Hammel Working lunch and introductions

1:30 - 2:30 pm Greg Hura and Michal Hammel Tour of the ALS, both SAXS and MX end stations

2:30 - 3:00 pm Scott Classen “Crystallographic Options at the ALS”

3:00 - 3:40 pm Michal Hammel and Daniel Rosenberg “Size Exclusion Coupled SAXS issues”

3:40 - 4:20 pm Greg Hura and Kathryn Burnett “High-throughput SAXS issues”

4:20 - 5:00 pm Hands on User Projects

saxs.png

scÅtter 1.7b has been released. scÅtter is JAVA-based software for the analysis of biological SAXS datasets.

DOWNLOAD

instructions and tutorial are available on the BIOISIS website.

For the MX endstation we've characterized the dependence of the direct beam on detector distance and 2-theta. We collected 4 sweeps of the detector from 120mm to 1600mm combined with 2-theta offsets from 0º up to 12º. These are the gnuplot 3D plots of the data.
xbeams.png ybeams.png
This set of 3D plots uses gnuplots pm3d settings to generate colorful versions:
xbeam3ds.png ybeam3ds.png
Click the images to view larger versions, and hit the "jump" to read the gory details of the polynomial equation used to determine x-beam and y-beam given any value of detector distance (CCD_Z) and 2-theta.
For older browsers, or non-flash enabled mobile browsers, we offer the old skool status page which has convenient small png files showing the last 24 hours of beamline data, but if you want to have a hands-on experience you might want to try out our new Google-style annotated time lines. If you're familiar with the Google finance web page where you can zoom in and explore the historical trends of the worlds financial markets you'll understand the coolness of this new tool.

izero_example.png

The SIBYLS beamline has recently been awarded 50,000 hours on the NERSC (National Energy Research Scientific Computing Center) to perform solution structure modeling using experimental SAXS data. Besides the usual ab-initio reconstructions programs a new approach in rigid body modeling BILBOMD has been parallelized on the NERSC supercomputer. It is commonly acknowledged that flexibility between domains of proteins is often critical for function. These motions, and proteins with large scale flexibility in general, are often not readily amenable to conventional structural analysis such as X-ray crystallography, NMR, or electron microscopy. We have developed an analysis tool using experimental SAXS measurements to identify flexibility and validate a constructed minimal ensemble of models which represent highly populated conformations in solution. The resolution is sufficient to address questions about the extent of the domain conformational sampling in solution? In our rigid body modeling strategy BILBOMD, molecular dynamics (MD) simulations are used to explore conformational space. A typical experiment involves  MD simulation on the domain connections at very high temperature, where the additional kinetic energy prevents the molecule from becoming trapped in a local minimum. The MD simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. A genetic algorithm is then used to identify the minimal ensemble (Minimal Ensemble Search, MES) required to best fit the experimental data. If you are interested in learning about and/or using this valuable SAXS analysis tool please contact Michal Hammel (MHammel at lbl dot gov).

The crystals server (an Apache Tomcat webapp) has been installed. The crystals webapp will allow you to upload an excel spreadsheet, containing a list of samples, to the SIBYLS beamline for use with DOMO. The spreadsheet will be automatically converted to an XML file and will become available to you via Blu-Ice once you start data collection. The webapp was developed at the SSRL and is in use at their Macromolecular Crystallography facility. If you have used the SAM robot at Stanford and uploaded your spreadsheet to their server then you will notice a distinct similarity.

ALS Ring Status

loading ...

Funding

Archives

Powered by Movable Type 5.2.13

March 2020

Sun Mon Tue Wed Thu Fri Sat
1 2 3 4 5 6 7
8 9 10 11 12 13 14
15 16 17 18 19 20 21
22 23 24 25 26 27 28
29 30 31