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DEER_orientation_dependent_analysis.zip (192.9 MB)

DEER orientation-dependent analysis scripts and metadata for the manuscript "Conformational information from orientationally selective Light-Induced Triplet–Triplet Electron Resonance spectroscopy"

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posted on 2023-04-17, 15:32 authored by Arnau BertranArnau Bertran

DEER_orientation_dependent_analysis.zip - Scripts and metadata for the orientation-dependent analysis of the DEER data presented in the manuscript "Conformational information from orientationally selective Light-Induced Triplet–Triplet Electron Resonance spectroscopy", for molecule Cu2-[3]. Experimental and computational methods are described in the METHODS section of the manuscript. DOI of the manuscript to be added after acceptance.


Contents:


- Cu2Pval4Pcis_gframe.pdb - DFT-optimized molecular geometry, in g-frame of Cu-porphyrin.

- Cu2Pval4Pcis_gframe.m - Script to parametrize molecular conformation for orientation-dependent DEER simulation.

- Cu2Pval4Pcis_gframe_OriDEERsim.txt - Parametrized molecular conformation for orientation-dependent DEER simulation.

- Input_OriPDSsim_multispin_magnetophotoselection_looping.m - Input script for orientation-dependent DEER simulations, to complete with data from Cu2Pval4Pcis_gframe_OriDEERsim.txt and parameters used for the DEER experiment. 

- OriPDSSim_multispin_magnetophotoselection_Pop.m, OriDEER_multispin_coordinates.m and foldoridist.m - Contain functions used in the orientation-dependent DEER simulation.

- OriDEERFitting.m - Script to fit simulated library of orientation-dependent DEER traces to the experimental form factors.


> form_factors - Dipolar traces background-corrected in DeerAnalysis, used for the fitting of the simulated library of DEER traces.


> Simulations_for_fitting - Simulated library of DEER traces based on the structural model, to be used for fitting.


> Results_fitting - Results from the fitting of the simulated library of DEER traces to the experimental form factor and scripts for post-processing.

- Results_CuPval4CuPcis_TOTALp_3971TOTALB0_5_Nfitting_50_casualN_815.mat - Results from fit, the index of the molecular conformation from the library added in each fitting iteration is stored in variable "J_store".

- plotting_form_factors_and_fits.m - Script to plot experimental and fitted form factors.

- counting_plotting_pvector_results_fitting.m - Script to post-process fit results and generate centre-to-centre distance distribution and sphere file for conformational plot.

- Cu2Pval4P_DEER_pvectors_fit.mat - Molecular conformations contributing to the best fit to the experimental form factors, as [phi,theta,r,alpha,beta,gamma], and corresponding weights.

- Cu2Pval4P_DEER_centre_centre_distance_distribution.mat - Centre-to-centre distance distribution resulting from the fit.

- CuPval4CuPcis_model_based_N100.bild - Sphere file for conformational plot.


> spin_spin_distribution

- spin_spin_distrib_all_pvectors.m - Script to generate spin-spin distance distribution from fit, taking electron spin delocalization into account.

- Cu2Pval4P_DEER_spin_spin_distance_distribution.mat - Resulting spin-spin distance distribution.


> angular_distributions

- phi_distribution.m - Script to generate angular distribution of phi values from fit (deer_phi_distribution_Cu2Pval4P.mat).

- theta_distribution.m - Script to generate angular distribution of theta values from fit (deer_phi_distribution_Pval4P.mat).

- plotting_all_angular_distributions.m - Script to compare phi and theta angular distributions obtained from DEER and LITTER for Cu2-[3] and [3], respectively.



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