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DIMPLE Analysis Script Documentation

Overview

This script executes PanDDA (Pan-Dataset Density Analysis) for crystallographic data analysis.

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

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

cd {{ inputDir }}
dimple my.mtz apo.pdb output-dir

# 
# inputDir is set to folder you selected. 
# change to any folder of your choice 
# 
inputDir={{ inputDir }}
inputDir=/data/dust/group/it/ReferenceData/p11/thaumatin/autoproc/thaumatin
mtzFile=truncate-unique.mtz
pdbFile=MONOMER.pdb

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

mkdir -p $ouputDir && cd $outputDir

dimple -M0 --slow --slow -f png $inputDir/$mtzFile $inputDir/$pdbFile $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/autoproc/thaumatin
mtzFile=truncate-unique.mtz
pdbFile=MONOMER.pdb

Output Setup

baseDir=/data/dust/user/$USER/dimple
outputDir=$baseDir/thaumatin
mkdir -p $outputDir && cd $outputDir

DIMPLE Command

dimple -M0 --slow --slow -f png $inputDir/$mtzFile $inputDir/$pdbFile $outputDir

Parameters

Files

  • mtzFile: Reflection data file (MTZ format)
  • pdbFile: Structure model file (PDB format)
  • outputDir: Results directory

Options

  • -M0: Disables molecular replacement
  • --slow: Runs more thorough refinement
  • -f png: Generates PNG format maps

Directory Structure

  • inputDir: Contains input files
  • baseDir: Base directory for output
  • outputDir: Specific output location