autoPROC Documentation : Introduction

Contents

• Features
• Authors and contributions

Features

• analysis of collections of images and image headers

• indexing of diffraction images

• determination of accurate cell parameters

• integration of a series of images

• processing of multi-sweep datasets:
  1. consistent indexing across sweeps, ensuring identical indexing for sweeps measured on the same crystal - taking multi-axis goniostat settings into account.
  2. internal scaling and merging of each sweep separately and (if applicable)
  3. joint scaling of all sweeps simultaneously and merging of related sweeps after that scaling

• production of files of intensities and amplitudes in various formats (MTZ, Scalepack)

• analysis of anomalous signal

• automatic determination of most likely space group symmetry

• Additional functionality is provided for topics like (among many others):
  • analysis of anisotropy (via our STARANISO package) and detection of multiple lattices
  • handling of e.g. ice-rings and multi-axis goniostats
  • automatic processing of multi-orientation, multi-wavelength, interleaved or inverse-beam datasets
  • automatic decision making regarding likely high-resolution limits

• A large number of tools and programs are included (about 70 scripts with over 50000 lines as well as 35 additional programs with over 240000 lines of Fortran, C and C++ code).

• Through this additional functionality and unique features, it attempts to provide an expert system for (1) high throughput and fully automated as well as (2) highly specialised and advanced data processing.

• It is widely used within the automatic processing options at beamlines and synchrotrons worldwide, processing hundreds of datasets a day in a fully automated manner.

• XDS (for data processing)
• AIMLESS (for scaling/merging)
• XSCALE (for scaling/merging) and
• POINTLESS (for data conversion and symmetry-analysis).
• MOSFLM (for a few legacy features destined to be deprecated)

Authors and contributions

• autoPROC:

  The tools, scripts and programs that make up the autoPROC framework are developed by C. Vonrhein, G. Bricogne, C. Flensburg, R. Fogh, P. Keller, W. Paciorek, A. Sharff and I. Tickle with input and feedback from all members of Global Phasing.

• simcal_predict:

  This tool is a particular use-mode of the simcal diffraction image simulation program written by Wlodek Paciorek and Claus Flensburg and extended as part of collaboration contract COL0044 between Global Phasing and the Diamond Light Source, specifically related to the I23 beamline.

• GPX2:

  The visualiser used for jointly display of images and enhanced predictions was initially developed by Wolfgang Brehm (while in the group of Kay Diederichs at University of Konstanz/DE) during an internship with Global Phasing during the Summer of 2014 with generous support by the MX group (particularly PX-III) of the Swiss Light Source.

• XDS, XSCALE:

  The data-processing program XDS is developed by W. Kabsch at the MPI for Medical Research, Heidelberg/DE and K. Diederichs at University of Konstanz/DE.

• AIMLESS, POINTLESS:

  The scaling program AIMLESS and the analysis program POINTLESS are developed by P. Evans at the LMB in Cambridge/UK.

• CCP4:

  Various programs and utilities from CCP4 are being used here - among them CAD, COMBAT, CTRUNCATE, F2MTZ, MTZ2SCA, MTZDUMP, MTZUTILS, REBATCH, REINDEX, RSTATS, SCALEIT, SFTOOLS, SORTMTZ, TRUNCATE, UNIQUE. Please see individual program documentation for details.