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Installation

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

Modules

  • ENM
    • chains
    • conformer
    • ddr
    • drag
    • ensemble
    • getAlphaFold
    • getpdb
    • remove
    • save
  • EnsembleAnalysis
    • addpdb
    • archive
    • asphericity
    • cluster
    • compare
    • coulomb
    • density
    • figures
    • flexibility
    • getens
    • get_MMMx
    • get_PED
    • get_Zenodo
    • inertiaframe
    • match
    • measures
    • order
    • property
    • put_MMMx
    • save
    • sort
    • subsample
    • superimpose
    • transition
    • zenodo
  • EnsembleFit
    • addpdb
    • archive
    • blocksize
    • csv
    • ddr
    • deer
    • discard
    • expand
    • figures
    • getpdb
    • initial
    • interactive
    • nnllsq
    • nofit
    • pdbsave
    • plot
    • plotgroup
    • pre
    • prerates
    • preratelinear
    • rmean
    • sans
    • save
    • saxs
    • zenodo
  • ExperimentDesign
    • addpdb
    • distributions
    • ENMpairs
    • expand
    • getAlphaFold
    • getens
    • hetpairlist, hetpairlist!
    • import
    • pairlist, pairlist!
    • plot
    • RBreference
    • RigiFlex
    • sitescan, sitescan!
    • trivariate
  • Flex
    • a_prop
    • acceptance
    • addpdb
    • b_prop
    • c_anchor
    • c_prop
    • clashtest
    • ddr
    • depth
    • expand
    • getpdb
    • loose
    • n_anchor
    • oligomer
    • parallel
    • save
    • scwrl4
    • sequence
    • skipto
    • verbose
  • FlexRNA
    • addpdb
    • anchor_3p
    • anchor_5p
    • ddr
    • expand
    • getpdb
    • save
    • sequence
    • skipto
    • verbose
  • Locate
    • cube
    • getAlphaFold
    • getpdb
    • grid
    • reference
    • save
  • Prepare
    • bilayer
    • center
    • chains
    • deselenate
    • getAlphaFold
    • getcyana
    • getens
    • getpdb
    • merge
    • mutate
    • oligomer
    • remove
    • renumber
    • repack
    • repair
    • replace
    • save
    • superimpose
    • symmetry
  • Rigi
    • ddr
    • maxsize
    • maxtime
    • maxtrials
    • models
    • nlink
    • parallel
    • plink
    • probability
    • rbtemplate
    • resolution
    • rigid
    • save
    • savepdb
    • separate off
    • superimpose
    • xl_percentage
    • xlink
  • Visualize
    • addpdb
    • color
    • colorscheme
    • density
    • execute
    • figures
    • getAlphaFold
    • getens
    • getPED
    • getZenodo
    • graphics
    • import
    • isosurface
    • label
    • normalize
    • script
    • show
  • YasaraRefine
    • addpdb
    • console
    • getens
    • getpdb
    • repack
    • save

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

Examples

  • Demo ExperimentDesign
    • Modules used
    • Source code
    • Functionality
    • Outputs
  • Demo Prepare
    • Modules used
    • Source code
    • Functionality
    • Outputs
  • Demo Rigi
    • Modules used
    • Source code
    • Functionality
    • Outputs
  • Demo FlexRNA
    • Modules used
    • Source code
    • Functionality
    • Outputs
  • Demo RigiFlex
    • Modules used
    • Functionality
    • Outputs

License

  • MIT License
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© Copyright MIT license 2020-, Gunnar Jeschke, Laura Esteban-Hofer

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