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The EMBL-HH Automated Crystal Structure Determination Platform

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The EMBL-Hamburg automated crystal structure determination platform is a system which contains several distinct decision-makers which executes a number of macromolecular crystallographic software programs to produce a software pipeline for automated and efficient crystal structure determination. A large number of possible structure solution paths are encoded in the system and the optimal path is selected by the decision-makers as the structure solution evolves. The processes have been optimised for speed so that the pipeline can be used effectively for validating the X-ray experiment at a synchrotron beamline. The platform offers SAD, S-SAD, SIRAS, 2W-MAD, 3W-MAD or 4W-MAD phase determination, molecular replacement (MR) and MRSAD phasing. It also includes RIP and MRRIP phasing and the phasing protocols have been optimised for UV induced radiation damage X-ray data.

Recently it has been extended to include MRSIRAS phasing.

Auto-Rickshaw comes in two flavours : a Beamline Version and an Advanced Version. Both versions use a similar GUI for input, but the Advanced Version requires the sequence information for the protein target in order to build the side chains.

The “Beamline Version” is explicitly designed for use in validation of the X-ray experiment at the synchrotron beamline as soon as the data have been collected and processed.

The “Advanced Version” can be used for phase improvement , a more complete model building and refinement if resolution of the anomalous data is better than 3.5 A The Advanced Version of the platform uses ARP/wARP, beta-version of SHELXE, RESOLVE and BUCCANEER.

The Auto-Rickshaw platform has been installed on a 64-processors Linux cluster and is remotely accessible to academic users via a web-server . It allows to evaluate the success of their X-ray diffraction experiments in the shortest possible time. This helps to ensure an efficient use of the beam time available. The platform is undergoing continuous development. This includes the improvement of the platform's decision makers, the incorporation of new functionalities as well as continuous software upgrades.

An emulation of the Auto-Rickshaw job submission.

Auto-Rickshaw server is freely accessible to users at academic institution upon online registration .

Last Edited: 25.09.2012 by Santosh Panjikar