Setup

Recommended:

git, conda, a command-line interface

For Windows: https://discuss.codecademy.com/t/setting-up-conda-in-git-bash/534473

Clone repository

Initialise git in your target folder.

Next, clone the repository:

git clone https://github.com/uhlmanngroup/SimulateNPCs.git

Import environment

conda env create -n NPC --file ENV.yml 
conda activate NPC 

Load the script

Run an IDE (e.g. spyder) in the folder that contains NPC_overview_and_CSV.py.

To open spyder:

spyder

Open NPC_overview_and_CSV.py in the IDE

Adapt NPC_overview_and_CSV.py

Modify the python code as follows:

Add the directory that contains NPC-overview_and_CSV.py

working dir = "path/to/directory"

Add the path to where output files should go

data_dir = "path/to/data/dir" 

Simulate NPCs

Change the seed to any number except 0 for reproducible results.

Select the Nup, N or C terminus, and model of interest:

nup = "NupOfInterest"
term = "N" # or "C"
model = "PDBModelOfInterest"

For a list of available options see preprint.

Set numbers of NPC to be simulated,

n_input = # any integer number

Adjust variability parameters Irregular variability:

mag = # any number >= 0 

Geometric variability Change radius, ring distance, twist angle, and ellipticity here. For example:

rnew = # change to new mean radius 
rsigma = # change to standard deviation on a Normal distribution to randomly change the radius 

Note on ellipticity: Due to spring interactions, the input value might not correspond to the output value. Generate elliptical NPCs with mag = 0 and read out minor/major axis ratio from an Overview plot with fitted ellipse.

Plotting

Change plotting parameters as follows to not show plots:

Overviewplot = {"plot": False , "ellipse": True, "circle": False}
Detailplot2D = {"plot": False, "showforce" : False}
XYvsTime = False
Detailplot3D = False

Overviewplot shows all simulated NPCs with fitted ellipse and/or circle Detailplot2D shows the first simulated NPC by default XYvsTime shows the change in x and y coordinates of nodes of a selected NPC over time. This can be used to ensure deformed NPCs are at equilibrium. Detailplot3D shows a 3D plot of a selected NPC.

Export data and features

Set to True to export simualted NPCs as a CSV file in the data directory:

MakeCSV = False

Set to True to export features of simulated NPCs:

featuresCSV = False 

Set to True to export features of individual NPC rings:

featuresCSV2 = False