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# alpha_viewer
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Class to view Alphafold models
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alpha_viewer is based on the alphafold2 colab notebook visualization. alpha_viewer includes functions to plot PAE (`plot_pae`) and pLDDT (`plot_pLDDT`). It also allows for coloring of the py3Dmol view based on pLDDT with `show_confidence`. alpha_viewer contains `.obs`, a pandas data-frame, that can be used for custom annotations based on aa postion within the chain(s). You can use a key of `.obs` to color the py3Dmol view of your protein(s) based that annotation with `show_annotation`.
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alpha_viewer is based on the alphafold2 colab notebook visualization. It automatically chooses the best available prediction. alpha_viewer includes functions to plot PAE (`plot_pae`) and pLDDT (`plot_pLDDT`). It also allows for coloring of the py3Dmol view based on pLDDT with `show_confidence`. alpha_viewer contains `.obs`, a pandas data-frame, that can be used for custom annotations based on aa postion within the chain(s). You can use a key of `.obs` to color the py3Dmol view of your protein(s) based that annotation with `show_annotation`.
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alpha-viewer has been tested to work with `monomer`, `monomer_ptm` and `multimer` models.
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So far it's sadly not possible to save the py3Dmol view for exporting.

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