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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), MRSAD and MRSIRAS phasing. It also includes RIP and MRRIP phasing and the phasing protocols have been optimised for UV induced radiation damage X-ray data.

MR/MRSAD phasing protocol of Auto-Rickshaw expolites latest version of AlphaFold Protein Structure Database for finding suitable search model if only sequence is provided.

Auto-Rickshaw (AR) comes in two flavours : a Beamline (Fast ) and an Advanced . 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 (Fast 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 5.5 A. The Advanced Version of the platform uses ARP/wARP, SHELXE, RESOLVE and BUCCANEER.

Automated crystal structure determination has been extended for multiple datasets which can be carried out using either the "multiscale" or "multidata" mode ( see the new entry page ). When a number of scaled datasets are available in mtz format, "multiscale" mode can be chosen for any phasing method. Other mode ("multidata") can be opted when raw images of several datasets have been integrated using XDS but not scaled. In either case, multiple AR jobs are launched using fast-version or advanced version by providing data directory upload for each set (Native/anomalous data) and by providing necessary input parameters. The above process requires directory for the processed intensity data to upload powered by dropbox (instructions given at each phasing protocol web page). Selection of the data is performed based on its unit cell and space group further followed by analysis of each dataset based on radiation damage and anomalous signal. If the anomalous signal of individual dataset is above the threshold, then the dataset is pushed for post data evaluation at the AR server using fast or advanced version otherwise the dataset is selected for clustering, merging and scaling. Similarly, each clustered and scaled data is analysed and pushed for data evaluation at the AR server for SAD phasing. Whereas for SIRAS or MAD phasing, decision is made based on isomorphous/dispersive and anomalous signal.

The Auto-Rickshaw platform has been installed on a multi-processors Linux cluster and is remotely accessible to academic users via a web-server . The platform is undergoing continuous development. This includes improvement of the platform's decision maker and the incorporation of new functionalities as well as continuous software upgrades.

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

Last Edited: 11.02.2022 by Santosh Panjikar