Scientific News
Auto-Rickshaw: faster, better, more
The Auto-Rickshaw automated crystal structure determination platform has received a further upgrade to include a combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination.
Evolution of the quality of the electron-
density maps and the model
completeness for a test case.
October 2009 - Auto-Rickshaw is a platform for automated crystal structure determination geared towards fast validation of X-ray diffraction data. The platform contains several distinct decision-makers which utilize a number of macromolecular crystallographic software programs to produce a software pipeline for automated and efficient crystal structure determination. The Auto-Rickshaw platform is installed on a 68-CPU core cluster at EMBL Hamburg and is remotely accessible to academic users via a web-server. This allows the user to evaluate the success of their X-ray diffraction experiments in the shortest possible time, ensuring an efficient use of the beam time available. The platform is free for academic users and currently has 531 registered users worldwide.
Since its release in 2005, Auto-Rickshaw has been under continuous development and the latest addition includes a combination of molecular replacement and single wavelength anomalous diffraction phasing (MRSAD). The complete MRSAD procedure includes molecular replacement, model refinement, experimental phasing, phase improvement and automated model building.
With an ever increasing number of three dimensional structures of biological macromolecules now available in the Protein Data Bank, and the associated potential search models, molecular replacement (MR) has become the predominant determination technique. As a result different approaches for MR have been developed and several good and easy-to-use MR programs have become available. Another important phasing method in macromolecular crystallography is single-wavelength anomalous diffraction (SAD). SAD is based on accurately collected anomalous intensity differences arising from the presence of heavy atoms. In a paper published today in Acta Crystallographica Section D, Santosh Panjikar and co authors from EMBL Hamburg demonstrate that by using a combination of MR and SAD, poor MR or SAD phases can be significantly improved. The details behind this upgrade, and the improvement over standard SAD or MR approaches is illustrated in the current paper by ten test cases taken from the JCSG diffraction database. The results showed that poor MR or SAD phases with phase errors larger than 70° can be improved using the MRSAD procedure, and that a large fraction of the model can be determined automatically from X-ray data extending to better than 2.6Å resolution.
Future developments of the Auto Rickshaw platform are already being planned. A number of additional tasks will be incorporated into the MR and MRSAD protocols including the use of other molecular replacement programs, the use of the SAD function in refinement and links to automatic data-collection software and automated data-processing systems.
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