Assembline
latest

Installation

  • System requirements
  • Installation with Anaconda
  • For developers

Input preparation

  • Organize data
  • JSON configuration file
  • Parameter file

Calculation of fit libraries

  • About fit libraries
  • Set up
  • Run
  • Analyze fits
  • Adding precomputed fitting libraries to JSON

Input structures

  • Input structures

Rigid bodies

  • Rigid bodies

Flexibility

  • Flexibility

Selectors

  • Selectors

Symmetry

  • Calculating symmetry
  • Defining symmetry
  • Applying symmetry
  • Symmetry constraints
  • Symmetry restraints

Restraints

  • Excluded volume (steric) restraints
  • Connectivity restraints
  • EM restraints
  • Crosslink restraints
  • Symmetry restraints and constraints
  • Interaction restraints
  • Distance restraints
  • Similar orientation restraints
  • Elastic network restraints
  • Parsimonious states restraints
  • Custom restraints

Running

  • Run the modelling
  • 1. Global optimization
  • 2. Recombinations
  • 3. Refinement
  • Running more
  • Modify and re-run

Analysis

  • Check the logs
  • Extract scores
  • Visualize models and trajectories
  • Quick test of convergence
  • Sampling exhaustiveness and precision

Notes

  • Glossary
  • Frequently asked questions
  • Troubleshooting
  • Tips and tricks
Assembline
  • »
  • Index

Index

C | P | R | S | T

C

  • constraint

P

  • particle

R

  • representation resolution
  • restraint

S

  • selector
  • series
  • subunit

T

  • transformation matrix

© Copyright Vasileios Rantos, Kai Karius, Jan Kosinski (EMBL Hamburg). Revision 55ff7cde.

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