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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.
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.
