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Installation

  • Source-code version
    • Requirements
    • Download
    • Matlab path
    • Getting started
  • Executable
    • Requirements
    • Download
    • Installation
    • Windows path
    • Getting started

Modules

  • ExperimentDesign
    • import
    • addpdb
    • getens
    • expand
    • plot
    • sitescan, sitescan!
    • pairlist, pairlist!
    • hetpairlist
    • distributions
    • ENMpairs
    • ENMpairs
    • RBreference
  • Prepare
    • getpdb
    • getcyana
    • save
    • center
    • symmetry
    • bilayer
    • mutate
    • repair
    • repack
    • deselenate
    • renumber
    • chains
    • replace
    • remove
    • merge
  • Rigi
    • rbtemplate
    • separate off
    • superimpose
  • Flex
    • getpdb
  • FlexRNA
  • ENM
  • EnsembleFit
  • EnsembleAnalysis
  • Locate
  • YasaraRefine

Input/output concept

  • Control files
    • Concept
    • Syntax
    • Restraint specification
  • Log files
  • Ensemble lists
  • Selection by address
    • Topology and ensemble addressing
    • Chains
    • Residues
    • Atoms
    • Water molecules
    • Conformers
    • Rotamers
    • Locations
    • Changes compared to MMM
    • Correspondence with ChimeraX

Spectroscopic labels

  • Rotamer libraries
    • Concept
    • Implementation
    • The get_label function
    • Set of libraries
    • Rotamer library format
  • Distance distributions
    • Reasons why distances are distributed
    • Computation of distance distributions

Third-party software

  • Third-party software
    • SCWRL4
    • ATSAS
    • MUSCLE
    • MSMS
    • HYDROPRO
    • DSSP
    • YASARA
  • Open concept
    • Open source/ open data concept
    • Branched pipeline concept

Examples

  • Example set
MMMx
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  • Search

© Copyright 2020-, Gunnar Jeschke, Laura Esteban-Hofer

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