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Updated README to clarify OPTICS features and usage instructions.
Updated README for clarity and consistency, including links and formatting improvements.
Add input and output sections for various scripts in README.
Clarified instructions for MAFFT installation on Windows.
Added a note about a simpler version of the intro to OPTICS.
added ability to map the comparison shap values onto two structures simultaneously + 'prettified' the output chimerax script
Updated image sizes in README and added warning about SHAP mode.
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full integration of mapping shap values to pdb structure files of opsins