How to visualise hydrophobicity of proteins using pymol?

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Rob Keller

Dear Andrew Debbarma Have a look at: Article A script to highlight hydrophobicity and charge on protein surfaces

If you have the pdb file of your protein why not use ChimeraX https://www.cgl.ucsf.edu/chimerax/ , I think it is way more user-friendly.

Best regards.

Marko Babić

I want to just add to Rob Keller's comment:

Chimera is a free tool that can show hydrophobic/hydrophilic surfaces with a few clicks instead of using a script for PyMOL.

Open Chimera, load your protein, go to Presets, then click "Interactive 3 (hydrophobicity, surface)".

Thats it.