These customized scripts are designed to extract diffusion-related information from smFRET and donor-only trajectory segments. The input data should first be analyzed and processed using smCellFRET v1.3 (doi:10.1038/s41592-021-01081-y).
Environment
- MATLAB scripts (*.m) tested with MATLAB R2020a
- Python scripts (*.py) tested with Python 3.7
Scripts Overview step 1: "smFRETRAP_traces_to_table": format transfer the fretTracesDif_bestFret.mat data to .txt format for further analysis, step 2: "selection_FRET_Donly.m": select and export trajectory segments as "FRET" and "Donly"(for donor only), step 3: "Diffusion_coefficient_dyn_loc_precision_motion_by_4pointsMSD.m": calculate the diffusion coefficient, dynamic localization precision, type of motion of the exported segments of trajectories, step 4: "jump_distance_angle.py": calculate Euclidean distance between two points within trajectories, calculate vector angle between three points within trajectories, step 5: "select_trace_belongs_to_pathway1 or 2.py": (optional) select the segments exported by step1 to either pathway1 or 2.
| Step | Script | Description |
|---|---|---|
| 1 | smFRETRAP_traces_to_table.m | Converts the output from smCellFRET (e.g. fretTracesDif_bestFret.mat) into a .txt format suitable for downstream analysis. |
| 2 | selection_FRET_Donly.m | Extracts and exports trajectory segments categorized as FRET or Donor-only (Donly). |
| 3 | Diffusion_coefficient_dyn_loc_precision_motion_by_4pointsMSD.m | Calculates the diffusion coefficient, dynamic localization precision, and type of motion (e.g., confined, free, or directed) for the exported trajectory segments. |
| 4 | jump_distance_angle.py | Computes the Euclidean distance between two points and the vector angle between three points within each trajectory. |
| 5 (optional) | select_trace_belongs_to_pathway1_or_2.py | Classifies exported trajectory segments (from Step 2) into Pathway 1 or Pathway 2 for further analysis. |