Edited on Oct 31, 2008

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The automar Data Processing Suite

automar is a revolutionary program package for processing single crystal diffraction data from proteins and small molecules. It comprises a full-featured GUI that supports all programs of the automar-suite. In addition, the integration and scaling programs of the CCP4-suite (ipmosflm), the XDS-suite and the HKL(R)-suite are supported. Suitable default parameters and menu driven choices are provided wherever possible. For difficult situations, expert settings are possible, too. The time and expertise required to process data is reduced to a minimum. Data processing has never been more straightforward.

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Highlights:

• Implementation of powerful new algorithms in the indexing, data integration and data scaling programs.
• Automatic parameter selection and update in the GUI - no typing required.
• Graphical visualization of all program steps.
• Autoindexing with extremely high success rates.
• Data integration with a minimum of selectable parameters.
• Quick and easy migration between several data integration packages: marProcess/marScale, mosflm/scala, xds/xscale and denzo/scalepack.
• Standardized input and output files.
• Highly suitable for inexperienced crystallographers due to well chosen defaults.

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Program steps:

• Setup:
  Diffraction parameters common to all program packages are entered here, e.g. cell axes, goniometer parameters, wavelength, etc.

• marPeaks:
  Choose spots for single crystal indexing of a from a single image, a range of consecutive images, or a series of non- consecutive images. The spot list is editable. Spots can be manually added or deleted by point and click. The program discriminates alpha1/alpha2-splitting when using Mo-radiation.

• marIndex:
  Unless there is a real problem with the crystal, the indexing program is going to index your diffraction pattern. As few as 20 reflection can be suffificient. The GUI presents an easily readable listing of cell and quality parameters for all 14 Bravais lattice types. If no space group has been supplied, the most likely one is picked. Indexing is very tolerant against errors in the beam center and the detector-to-crystal distance.
  The indexing results can be fed directly into data integration programs marProcess, ipmosflm, xds or denzo. All refined parameters are loaded automatically into the GUI.

• marStrategy:
  The pogram finds the most suitable staring angle for a data collection. The quickest way of obtaining a complete data set is presented at one glance.

• marProcess:
  The data integration program marProcess implements the "seed-skewness-method" (Bolotovsky et al., J. of Applied Crystallography, 28, pp-95 (1995)) and combines it with traditional profile fitting. This technique works extremely well for both protein and small molecule data and reliefs users from having to determine integration box sizes manually. Spot sizes and diffraction parameters are adapted on-the-fly and make reprocessing obsolete.

• marPost/marScale:
  Program marPost sums up partial reflections from the integration step. It also does a post-refinement of crystal orientation, mosaicity, divergence and cell parameters.
  Program marScale merges and analyzes the integrated data. The most important results are displayed in the GGUI and allow for quick evaluation. A wide variety of 2D-plots are also available.

• Truncate/Convert:
  After scaling, tools are offered to feed the intensity data into program "truncate" out of the CCP4-suite to convert them into structure factors. A variety of format conversion programs is also available to convert output of the automar suite or other supported program packages into files suitable for the CCP4-package, SHELX, CNS, etc.

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Downloads and Manuals:

• automar manual (html)
• automar tutorial "step-by-step" (pdf)
• marIndex manual (pdf)
• marProcess/marPost/marScale manual (pdf)

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