PanDDA Analysis Script Documentation

Overview

This script uses DIMPLE (Difference Map Pipeline) to analyze crystallographic data by comparing diffraction data (MTZ) with a reference structure (PDB) to identify structural differences and validate molecular models.

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

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

#
# workdir is the location for the panda output
# change it for example to   
#     {{ inputDir }}                 to get ouput in the location of the pandda input data
#     /data/dust/user/$USER/pandda   to get output in DUST space, etc
#
workdir=$PWD
mkdir -p $workdir

pandda.analyse data_dirs={{ inputDir }} pdb_style='*.dimple.pdb' cpus=$(nproc)

{# =============================================================================================================== #}
{# 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.

Main Execution

workdir=$PWD
mkdir -p $workdir
pandda.analyse data_dirs={{ inputDir }} pdb_style='*.dimple.pdb' cpus=$(nproc)

Key components:

• workdir: Output location for PanDDA results
• mkdir -p $workdir: Creates output directory
• pandda.analyse: Main analysis command with parameters:
  • data_dirs: Input directory containing datasets
  • pdb_style: Pattern for PDB files (*.dimple.pdb)
  • cpus: Utilizes all available processors

Output Location Options

1. Current directory: workdir=$PWD
2. Input data location: workdir={{ inputDir }}
3. Custom location: workdir=/data/dust/user/$USER/pandda

System Cleanup

{- applicationUnload -}
{- systemUnload -}

Unloads system modules and applications.