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Autoproc Script Documentation

Overview

This script processes crystallographic diffraction data from HDF5 files using autoPROC, automating the data reduction pipeline from raw images to processed reflection data.

# Preambles start - Avoid touching these unless required. #}
  {- systemLoad -}
  {- applicationLoad -}
{# Preambles end #}

{# =============================================================================================================== #}
{# Start the job - change as required                                                                              #}
{# =============================================================================================================== #}

#
# inputDir is set to folder you selected. expected location of images or h5-files
# change to any folder of your choice 
# 
inputDir={{ inputDir }}
inputDir=/data/dust/group/it/ReferenceData/p11/thaumatin/rotational_002
inFile=thaumatin_rotational_002_master.h5

# Note: outputDir must not exist! 
baseDir=/data/dust/user/$USER/autoproc
outputDir=$baseDir/thaumatin

mkdir -p $baseDir && cd $baseDir

symmetry="P 91"
unit_cell="93.170 93.170 361.370 90.00 90.00 90.00" 

process symm=$symmetry cell=$unit_cell -h5 $inputDir/$inFile -d $outputDir 
process -h5 $inputDir/$inFile -d $outputDir 

{# =============================================================================================================== #}
{# End of job                                                                                                      #}
{# =============================================================================================================== #}

{# Postambles start - Avoid touching these unless required. #}
  {- applicationUnload -}
  {- systemUnload -}
{# Postambles end #}

Script Structure

System Setup

{- systemLoad -}
{- applicationLoad -}

Loads required system modules and applications.

Input Configuration

inputDir=/data/dust/group/it/ReferenceData/p11/thaumatin/rotational_002
inFile=thaumatin_rotational_002_master.h5

Crystal Parameters

symmetry="P 91"
unit_cell="93.170 93.170 361.370 90.00 90.00 90.00"

Output Setup

baseDir=/data/dust/user/$USER/autoproc
outputDir=$baseDir/thaumatin

Processing Commands

process symm=$symmetry cell=$unit_cell -h5 $inputDir/$inFile -d $outputDir
process -h5 $inputDir/$inFile -d $outputDir

Key Parameters

  • inFile: HDF5 master file
  • symmetry: Space group
  • unit_cell: Unit cell parameters
  • outputDir: Results directory (must not exist)