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

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. <br> Contents: <br> - 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. <br> &gt; form_factors - Dipolar traces background-corrected in DeerAnalysis, used for the fitting of the simulated library of DEER traces. <br> &gt; Simulations_for_fitting - Simulated library of DEER traces based on the structural model, to be used for fitting. <br> &gt; 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. <br> &gt; 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. <br> &gt; 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. <br> <br>

DEER_orientation_dependent_analysis.zip —— 本压缩包备有用于对论文《Conformational information from orientationally selective Light-Induced Triplet–Triplet Electron Resonance spectroscopy》（译：《来自取向选择性光诱导三重态-三重态电子共振光谱的构象信息》）中呈现的双电子-电子共振（Double Electron-Electron Resonance，DEER）数据开展取向依赖性分析的脚本与元数据，研究体系为分子Cu₂-[3]。实验与计算方法详见论文的“方法（METHODS）”章节。论文的DOI将在录用后补充。

内容如下：
- Cu2Pval4Pcis_gframe.pdb：经密度泛函理论（Density Functional Theory，DFT）优化的蛋白质数据库（Protein Data Bank，PDB）格式分子几何构型文件，采用铜卟啉的g-frame坐标系。
- Cu2Pval4Pcis_gframe.m：用于为取向依赖性DEER模拟参数化分子构象的MATLAB脚本。
- Cu2Pval4Pcis_gframe_OriDEERsim.txt：用于取向依赖性DEER模拟的参数化分子构象文件。
- Input_OriPDSsim_multispin_magnetophotoselection_looping.m：取向依赖性DEER模拟的输入脚本，需结合Cu2Pval4Pcis_gframe_OriDEERsim.txt中的数据与DEER实验所用参数完成配置。
- OriPDSSim_multispin_magnetophotoselection_Pop.m、OriDEER_multispin_coordinates.m 与 foldoridist.m：包含取向依赖性DEER模拟所需的核心功能函数。
- OriDEERFitting.m：用于将取向依赖性DEER轨迹的模拟库拟合至实验形状因子的MATLAB脚本。

> form_factors：在DeerAnalysis软件中经背景校正的偶极轨迹，用于DEER轨迹模拟库的拟合操作。
> Simulations_for_fitting：基于结构模型构建的DEER轨迹模拟库，用于后续拟合流程。
> Results_fitting：将DEER轨迹模拟库拟合至实验形状因子所得的全部结果，以及用于结果后处理的配套脚本。

- Results_CuPval4CuPcis_TOTALp_3971TOTALB0_5_Nfitting_50_casualN_815.mat：拟合结果文件，每次拟合迭代中来自构象库的分子构象索引存储于变量"J_store"中。
- plotting_form_factors_and_fits.m：用于绘制实验与拟合所得形状因子的MATLAB脚本。
- counting_plotting_pvector_results_fitting.m：用于后处理拟合结果、生成分子中心间距分布与构象绘图所需球体文件的MATLAB脚本。
- Cu2Pval4P_DEER_pvectors_fit.mat：对实验形状因子具有最佳拟合效果的分子构象数据，以"[phi,theta,r,alpha,beta,gamma]"格式存储，同时包含对应的权重参数。
- Cu2Pval4P_DEER_centre_centre_distance_distribution.mat：由拟合结果推导得到的分子中心间距分布文件。
- CuPval4CuPcis_model_based_N100.bild：用于构象可视化绘图的球体文件。

> spin_spin_distribution：
- spin_spin_distrib_all_pvectors.m：用于从拟合结果生成自旋-自旋距离分布的MATLAB脚本，计算过程中需考虑电子自旋离域效应。
- Cu2Pval4P_DEER_spin_spin_distance_distribution.mat：最终得到的自旋-自旋距离分布文件。

> angular_distributions：
- phi_distribution.m：用于从拟合结果生成phi值角分布的MATLAB脚本（输出文件为deer_phi_distribution_Cu2Pval4P.mat）。
- theta_distribution.m：用于从拟合结果生成theta值角分布的MATLAB脚本（输出文件为deer_phi_distribution_Pval4P.mat）。
- plotting_all_angular_distributions.m：用于对比Cu₂-[3]的DEER角分布与[3]的LITTER角分布的MATLAB脚本。