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DeerLab
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User Guide

  • Installation
  • User Guide
    • Basics
    • Getting Started
    • Modeling
    • Fitting
    • Theory
  • Advanced
    • Modeling Guide
    • Fitting Guide
    • Uncertainty Guide
  • Examples
    • Simulating a 4-pulse DEER signal
    • Simulating a 5-pulse DEER signal
    • Simulating a three-pathway 4-pulse DEER signal
    • Basic analysis of a 4-pulse DEER signal
    • Basic analysis of a RIDME signal
    • Analysis of a 4-pulse DEER signal with a compactness penalty
    • Bootstrapped confidence intervals in routine analysis
    • Basic analysis of a 4-pulse DEER signal with a bimodal Gaussian model
    • Basic fitting of a 5-pulse DEER signal
    • Distance restraints from 4-pulse DEER data, non-parametric distribution
    • Validating multi-pathway models based on the data
    • Analysis of a 4-pulse DEER signal with multiple dipolar pathways
    • Analysis of a 6-pulse DQC signal with multiple dipolar pathways
    • Global fitting of multiple 4-pulse DEER signals, non-parametric distribution
    • Analysis of a 5-pulse DEER signal with multiple dipolar pathways
    • Basic analysis of a sparsely sampled 4-pulse DEER signal
    • Comparing the analysis with and without compactness criterion
    • Global fitting of multiple different DEER signals
    • Analyzing data with crossing echoes robustly
    • Analysing the selection of regularisation parameter
    • Simulating polarization effects on low-temperature DEER
    • Identifiability analysis of a 4-pulse DEER signal via the profile analysis method
    • Comparing confidence intervals for regularization results
    • Simulating orientation selection effects in dipolar signals
    • Fitting Gaussians to a non-parametric distance distribution fit
    • Profile analysis in routine analysis
    • Multi-Gaussian analysis of a dipolar signal
    • Global fitting of a two-state model to a series of DEER traces
    • Dipolar pathways model selection
    • Fit a polynomial force field to a dipolar signal
    • Analyzing pseudo-titration (dose-response) curves with non-parametric distributions
    • Global analysis of 5-pulse DEER on a liquid-droplet protein system
  • Models
    • deerlab.ex_3pdeer
    • deerlab.ex_4pdeer
    • deerlab.ex_rev5pdeer
    • deerlab.ex_fwd5pdeer
    • deerlab.ex_sifter
    • deerlab.ex_dqc
    • deerlab.ex_ridme
    • deerlab.dd_gauss
    • deerlab.dd_gauss2
    • deerlab.dd_gauss3
    • deerlab.dd_rice
    • deerlab.dd_rice2
    • deerlab.dd_rice3
    • deerlab.dd_gengauss
    • deerlab.dd_skewgauss
    • deerlab.dd_cos
    • deerlab.dd_wormchain
    • deerlab.dd_wormgauss
    • deerlab.dd_randcoil
    • deerlab.dd_sphere
    • deerlab.dd_spheresurf
    • deerlab.dd_spherepoint
    • deerlab.dd_shell
    • deerlab.dd_shellshell
    • deerlab.dd_shellsphere
    • deerlab.dd_shellvoidshell
    • deerlab.dd_shellvoidsphere
    • deerlab.dd_circle
    • deerlab.dd_triangle
    • deerlab.dd_uniform
    • deerlab.bg_hom3d
    • deerlab.bg_hom3dex
    • deerlab.bg_homfractal
    • deerlab.bg_hom3d_phase
    • deerlab.bg_hom3dex_phase
    • deerlab.bg_homfractal_phase
    • deerlab.bg_exp
    • deerlab.bg_strexp
    • deerlab.bg_sumstrexp
    • deerlab.bg_prodstrexp
    • deerlab.bg_poly1
    • deerlab.bg_poly2
    • deerlab.bg_poly3
  • Reference Index
    • deerlab.Model
    • deerlab.Parameter
    • deerlab.Penalty
    • deerlab.FitResult
    • deerlab.UQResult
    • deerlab.ExperimentInfo
    • deerlab.fit
    • deerlab.merge
    • deerlab.link
    • deerlab.lincombine
    • deerlab.relate
    • deerlab.regoperator
    • deerlab.selregparam
    • deerlab.noiselevel
    • deerlab.whitegaussnoise
    • deerlab.diststats
    • deerlab.correctphase
    • deerlab.bootstrap_analysis
    • deerlab.profile_analysis
    • deerlab.snlls
    • deerlab.fnnls
    • deerlab.cvxnnls
    • deerlab.goodness_of_fit
    • deerlab.dipolarmodel
    • deerlab.dipolarpenalty
    • deerlab.deerload
    • deerlab.dipolarkernel
    • deerlab.dipolarbackground
    • deerlab.fftspec
    • deerlab.distancerange
    • deerlab.store_pickle
    • deerlab.read_pickle
    • deerlab.sophegrid
    • deerlab.choleskycovmat
    • deerlab.hccm
    • deerlab.Jacobian
    • deerlab.nearest_psd
    • deerlab.movmean
    • deerlab.ovl
    • deerlab.der_snr
    • deerlab.formatted_table

About

  • Contributing
  • Release Notes
  • License
  • Publications
  • Funding
  • Github
  • Discussion Board
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Basic - Simulations

These are basic examples for performing dipolar EPR simulations in DeerLab.

Simulating a 4-pulse DEER signal

Simulating a 4-pulse DEER signal

Simulating a 5-pulse DEER signal

Simulating a 5-pulse DEER signal

Simulating a three-pathway 4-pulse DEER signal

Simulating a three-pathway 4-pulse DEER signal
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Simulating a 4-pulse DEER signal
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Examples
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