polysome_mef

Python scripts for ribosome nearest neighbor distance measurements used in

Fedry et al., Visualization of translation reorganization upon persistent collision stress in mammalian cells

Dependencies

Please make sure the following Python3 packages are present:

• NumPy
• eulerangles
• Matplotlib

Quick start

From the top folder of this repository, execute

gunzip ./data/untreated_ref120.star.gz
python3 split_star.py ./data/untreated_ref120.star
python3 compute_data.py ./data/*.tomostar.star
python3 distances.py

This produces the plot of the nearest neighbor distances

./data/Untreated.png

for the control dataset.

Usage

First, unpack the star file

gunzip ./data/untreated_ref120.star.gz

File ./data/untreated_ref120.star is Relion refine star file with coordinates and angles of all ribosomes in the control dataset.

Next, split the star file into star files per tomogram

python3 split_star.py ./data/untreated_ref120.star

This generates files ./data/*.tomostar.star for each tomogram in the dataset.

For each tomogram, compute the data of interest by

python3 compute_data.py ./data/*.tomostar.star

This generates json files ./data/*.json.
The json file is a list of dictionaries, where each dictionary corresponds to a single ribosome, for example:

{ "starfile_row": "...", 
  "xyz": [1459.0, 812.0, 758.0], 
  "rot": -13.40005, 
  "tilt": 72.359731, 
  "psi": 177.817038, 
  "x0y0z0": [0.9149096774193549, -8.739467741935485, 0.6061539170506912], 
  "xyz_entry": [1455.1453325112989, 819.5896008702275, 770.0695129367426], 
  "xyz_exit": [1465.2255310348175, 808.8411191417952, 757.66496787213], 
  "index": 0, 
  "dmin_next": 35.60744083483111, 
  "dmin_next_index": 124, 
  "dmin_prev": 30.79511464048548, 
  "dmin_prev_index": 127, 
  "dmin": 30.79511464048548, 
  "dmin_index": 127 
}

Here, xyz_entry and xyz_exit are coordinates in pixels in the original map of the ribosome entry and exit sites, index is the index of the ribosome in a tomogram, dmin is a distance in pixels to the nearest neighbor, and dmin_index is the index of the nearest neighbor ribosome. Similarly, dmin_next and dmin_prev are distances to the next and previous ribosome in the polysome.

Finally, we plot the distribution of all nearest neighbor distances dmin in the dataset by

python3 distances.py