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If you are asking for the ability to edit/mutate structures, I prefer to keep the focus on visualization (but am very willing to accept pull requests from contributors - this is just a line I draw on how I will spend my very limited development time). If there is a specific way you want to visualize these modified residues, that is something I could look into.
3Dmol is awesome for visualizing protein.
Is it possible to have post-translational modifications (PTMs) features in 3Dmol?
Just like the PyTMs for PyMOL.
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