Assembline - Assembly line of macromolecular assemblies!

Assembline manual

Installation

• System requirements
• Installation with Anaconda
  • Install dependencies
  • Install Anaconda
  • Create virtual Anaconda environment
  • Install Python dependencies
  • Install Gnuplot
  • Install R
  • Install Assembline
• For developers
  • Clone our repositories:
  • Clone PDBX and PDB-TOOLS
  • Setup before running
  • Explanations:

Input preparation

• Organize data
• JSON configuration file
  • Creating JSON file
  • Series and copies
  • Selectors
  • Paths
• Parameter file
  • Creating the parameter file
  • Parameters

Calculation of fit libraries

• About fit libraries
• Set up
• Run
• Analyze fits
  • Check if run correctly
  • Generating fitted PDBs
• Adding precomputed fitting libraries to JSON

Input structures

• Input structures

Rigid bodies

• Rigid bodies

Flexibility

• Flexibility

Selectors

• Selectors

Symmetry

• Calculating symmetry
  • Method 1
  • Method 2
• Defining symmetry
  • Using a symmetry axis information
  • Using transformation matrix
• Applying symmetry
• Symmetry constraints
• Symmetry restraints

Restraints

• Excluded volume (steric) restraints
• Connectivity restraints
• EM restraints
  • Precomputed EM fits
  • FitRestraint
  • EnvelopePenetrationRestraint
  • ExcludeMapRestraint1
  • CloseToEnvelopeRestraint
  • EnvelopeFitRestraint
• Crosslink restraints
  • Loading crosslink data
  • Defining the restraints
  • Parameters
• Symmetry restraints and constraints
• Interaction restraints
• Distance restraints
• Similar orientation restraints
• Elastic network restraints
• Parsimonious states restraints
• Custom restraints

Running

• Run the modelling
  • Introduction
  • A single run
  • Multiple runs
  • Assembline.py options
  • Checking if everyhting runs correctly
• 1. Global optimization
• 2. Recombinations
• 3. Refinement
  • Refine the top-scoring models from previous modelling modes/runs
  • Refine a single model
  • Refine multiple models
• Running more
• Modify and re-run
  • Typical adjustments that need to be done:
  • Was the calculation quick?

Analysis

• Check the logs
• Extract scores
  • Plot histograms of all scores
• Visualize models and trajectories
  • Create CIF format file for top models
  • Create CIF format file for a specific model
  • Rebuilding flexible beads
  • Create PDB for top models
  • Create separate PDB files for rigid bodies
  • Other options
  • Visualize the top model(s) in Chimera and Xlink Analyzer
  • Visualize the optimization trajectory of the top model(s) in Chimera and Xlink Analyzer
• Quick test of convergence
• Sampling exhaustiveness and precision

Notes

• Glossary
• Frequently asked questions
• Troubleshooting
• Tips and tricks
  • Speeding up calculations