Automated PX Data Collection and Processing at Synchrotron Beamlines

Project Description

The primary objective is the provision of software that will allow fully automated collection and processing of diffraction data, including rapid crystal screening. Ultimately the project will be extended to include automated sample loading and a project management system, which will enable a large number of crystals from a number of different projects to be handled without any manual intervention.

Automation will be achieved by providing a direct communication pathway between existing data processing software and beamline control software. This communication will be managed by a new software package termed the "Expert System" (Fig.1). This program will also take critical decisions about the data collection based on information provided by the data processing software and some basic parameters relating to the project that will be supplied by the user.

Figure 1

The modular nature of such a system will simplify installation on different beamlines, (which will typically have different beamline control software) and allow the use of different data processing software (providing it has the necessary functionality).

The Expert System will maintain overall control, issuing instructions to both the beamline control software and the data processing software. These commands will be in a high level language (see Appendix), which will be "translated" into commands that are understood by the respective software packages by a translator/server, which will also handle the communication protocol. These translator/servers will be specific for each beamline/processing software package. The Expert System will also receive information from both the beamline control and data processing software. This information, which will conform to a pre-defined standard, will be used to make decisions, for example about whether a particular crystal is suitable for data collection, and if so, about the optimal data collection parameters (resolution, exposure time etc.).

The success or failure of the autoindexing of one or more test images will be used as the initial indicator of crystal quality. This will be judged by the rms error in predicted spot positions and the fraction of spots that are rejected from indexing or refinement. If the autoindexing is successful, the crystal mosaicity will be estimated and the test images will be integrated to obtain an indication of data quality and the effective resolution, deduced from the <I/sig(I)> values as a function of resolution. A data collection strategy based on the deduced Laue group (with the lowest possible symmetry) will also be calculated. The Expert System will use this information to determine if the crystal is really suitable for data collection (for example, if the required resolution can be achieved) and to determine data collection parameters. It will then instruct the beamline software to collect the required images, and the data processing software to process the images as they are collected.

Implementation

Phase I. In this phase, the Expert System will simply provide a communication pathway between the data processing software (a suitably modified version of MOSFLM) and the beamline control software (a modified version of the ESRF software PRODC or the SRS software PXGEN). To simplify use of the system, access will be provided via a new button "Characterise Crystal" on the existing PRODC/PXGEN GUI. This will send an instruction to the Expert System, which will then send instructions to PRODC/PXGEN to collect two oscillation images separated by 90° in phi. It will then send instructions to MOSFLM to autoindex the images, estimate the mosaicity, integrate the images and calculate a data collection strategy. This information will be displayed in the message window of the PRODC/PXGEN GUI.

Phase II. The parameters of the data collection determined by the Expert System, will be presented to the user in a GUI (either a new GUI or an extension of PRODC/PXGEN) where they can be edited by the user. This will allow the user to override suggested rotation ranges, exposure times, oscillation angles etc. A new button will allow the user to collect the data using these parameters.

Phase III. An additional button will allow the user to integrate the images as they are collected. Information about the results of the integration (eg <I/sig(I)> as a function of resolution) will be fed back to the GUI from the data processing. Results of merging the data will also be displayed.

Phase IV. Implementation of fully automated data collection and processing. A single button will activate initial characterisation of the crystal, and providing that user-defined criteria regarding resolution, mosaicity etc. are met, the data will be collected and integrated without any user intervention.

Phase V. Automated sample loading (including crystal centring in the beam) and a project management system will be integrated with the Expert System. This will allow rank ordering of multiple crystals based on their diffraction properties, and fully automated beamline operation.

Appendix

1. High level commands. See minutes of meeting held on 11 June 2001.

2. Communication protocols. Commands will be structured in XML, and passed via sockets using HTTP. See minutes of meeting held on 19 September 2001.