Jupyter notebooks for ribosome-membrane orientation and polysome organization analysis used in Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome.
Notebook: ribomove/ribocone.ipynb
Main steps:
- detect membrane density in an annular region of each class volume
- fit the in-plane membrane direction by PCA
- estimate through-plane membrane tilt across Z-slices
- project 3D normal deviations onto a 2D tangent plane
- plot membrane plane intersections and angular deviation density
Notebook: polysome/poly.ipynb
Main steps:
- read ribosome coordinates and angles
- build candidate ribosome-ribosome edges using KDTree distance search
- filter neighbors by center-to-center distance and SO(3) orientation similarity
- keep connected components with degree ≤ 2 (no ribosome in a polysome can have three neighbors)
- plot tomogram map-backs, selected polysome examples, and chain-length distributions
numpy
pandas
matplotlib
scipy
starfile
mrcfile
jupyter
Open the notebooks in Jupyter and edit the parameter block at the top of each notebook:
jupyter notebook ribomove/ribocone.ipynb
jupyter notebook polysome/poly.ipynbMIT