Collection of scripts for the setup and analysis of simulations relating to the publication: Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms
This contains scripts associcated with the geenral analysis of simulations. Typically these produce .pkl files that can be used by plotting scripts located in the plotting_scripts directory.
An example of calc_distances.py:
python scripts/analysis_scripts/calc_distances.py -pdb_file input_file.gro -traj_path path/to/trajectories/ -residue_pair 219 208 -plot_hist True -cog True -system_name Double -save_name min_dist_R219_E208
This contains a collection of scripts to plot all results together.
An example of plot_all_distancs.py:
python scripts/plotting_scripts/plot_all_distances.py -data_files 0_WT/207_208_dist_H_carboxy.pkl 1_D211K/207_208_dist_H_carboxy.pkl 2_T207S/207_208_dist_H_carboxy.pkl 3_double_D211K_T207S/207_208_dist_H_carboxy.pkl -save_name min_207_208_H_carboxy_distance_v2 -xlabel "T/S207 - E208 minimum distance" -kde True
This contains a collection of PyMol scripts used to generate publication-ready figures of key residues in the voltage-sensor domain.
This contains a helper script to remove water present in the membrane when creating an membrane-embedded protein system.