July 17 Hackathon minutes

[jonathanfischer97]

Sphere hexamer fitting for Gag

model/spherical_assembly

• “Yufeng_Progress_Report”

• Modifies bond angles and coordinates to align PDB structure on sphere

• Hyperparameters:

  • User must define sphere radius

• gagReshape.py is what Matt used, originally Yiben’s

  • Input: Trihexagonal lattice Gag PDB structure
  • Better than Yufeng’s code
  • Hardcoded for Gag but very accurate

@sangmk Add checkbox on website for sphere vs non-sphere

Problem: Fitting a circle

• RMSD
• Fit curvature 1/r instead of radius r?

How to calculate the radius of gyration from atomic structure?

• Stick with current method as defined in course_grain.py

Methods

repeated_chain_detection.py

• Try on actin, ...

1. mmCIF, elif
2. sequence alignment (> 95%), elif
3. structure alignment

Next step is repeat regularization

#59 regularize_homologous_chains