autoPROC Documentation

Contents

1. Introduction
   • Features
   • Authors and contributions

2. autoPROC distribution
   • Access to autoPROC
   • Installation
   • Testing installation

3. Image file formats

4. Usage
   • process
     • Command line
   • Recommended minimum user input
     • Beam centre
     • Beam stop
   • Additional parameters

   • aP_scale (scaling module)

   • Others tools and programs
     • aP_check
     • beam8.sh
     • check_indexing
     • cmpmat
     • combine_files
     • find_images
     • imgdate.sh
     • imginfo
     • mrfana

5. Examples
   • autoPROC Wiki
   • reference card (PDF)
   • Simple one-liners
     • Simple case with images in current directory and correct image headers
     • Images are in different location
     • Beam centre in image header is wrong
     • Problematic diffraction pattern or challenging project
     • Running on data from a specific beamline

   • When encountering problems
     • Getting started
     • During indexing
     • During integration
     • During scaling

6. Advanced features
   • Setting parameters
     • On the command-line
     • In a macro file(s)
   • Sorted list of parameters

7. Interpreting autoPROC output
   • Introduction
   • Step-by-step
     • Preparation
       • BeamCentreFrom setting
       • Sweep/dataset definition
     • Spot search and indexing
       • Iterative indexing
       • Visualisation with GPX2
       • Unindexed spots (SPOT_never-indexed.noHKL.png)
     • Initial integration and space group determination
       • Image scale factor (scale.png)
       • Mosaicity and beam divergence (divergence-mosaicity.png)
       • Space group assignment
       • Statistics
       • Anomalous signal
     • Integration
       • Overloaded reflections
       • Introduction to plots
       • Changes to orientation matrix (ngle_cell_axis_ABC.png and ngle_cell_axis0_ABC.png)
       • Change in cell dimensions/volume (cell_axes_devmean.png)
       • Crystal to detector distance (distance.png)
       • Direct beam position and detector origin (detector_center_origin.png)
       • Standard deviation on spot position and spindle value (standard_deviation.png)
     • Scaling and merging
       • Overall statistics for AIMLESS scaling
       • High-resolution criteria
       • Overall statistics for XSCALE scaling
       • STARANISO
       • Overall statistics for measurements
       • Overall statistics for observations
       • REMARK 200 (remark200.pdb)
     • Multi-sweep datasets
       • Introduction
       • Effect on processing second and following sweeps
       • Multi-axis goniostats (kapparot)
       • Final scaling and merging of all data
   • Plots and summary.html
     • Locating plots
     • How to view plots
   • GPX2
   • Output reflection data

8. Computing and visualising predictions
   • Introduction
   • Computation of positions and shapes of reflections with simcal_predict
   • Visualisation with GPX2

9. Scaling options
   • Introduction
   • Current default scaling mode
   • AIMLESS-only scaling path
   • XDS/XSCALE-only scaling path
   • Common features

10. Appendix 1: parameter list

11. STARANISO